![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 17 months ago
Last modified 17 months ago
#15680 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Analysis | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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",
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"procStartAbsTime" : 2424915584763,
"coalitionID" : 1886,
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"build" : "21D62",
"releaseType" : "User"
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"captureTime" : "2024-07-25 19:21:11.4453 -0400",
"incident" : "B8696695-4D5A-47B2-A79F-1DDE8DDEE8F8",
"bug_type" : "309",
"pid" : 47758,
"procExitAbsTime" : 6315241696595,
"translated" : false,
"cpuType" : "ARM-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.1","CFBundleVersion":"1.7.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"55613E8D-1A18-5B6D-A189-C7104B04AEA8","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "E2274857-0D38-62EA-C0DA-B536BC6AE048",
"wakeTime" : 1698,
"sleepWakeUUID" : "34FAFA9F-3617-41B5-99AC-1305674EDE4F",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4369629184\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 104734000-104738000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4369629184\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 104734000-104738000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
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"faultingThread" : 33,
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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
> select #9/C:462
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #9/C:463
44 atoms, 48 bonds, 2 residues, 1 model selected
> select add #9/C:464
66 atoms, 72 bonds, 3 residues, 1 model selected
> select add #9/C:465
88 atoms, 96 bonds, 4 residues, 1 model selected
> select add #9/C:466
111 atoms, 121 bonds, 5 residues, 1 model selected
> show #!1 models
> hide #!1 models
> select subtract #9/C:463
89 atoms, 97 bonds, 4 residues, 1 model selected
> select subtract #9/C:462
67 atoms, 73 bonds, 3 residues, 1 model selected
> select add #9/C:463
89 atoms, 97 bonds, 4 residues, 1 model selected
> show #!1 models
> hide #!1 models
> select subtract #9/C:463
67 atoms, 73 bonds, 3 residues, 1 model selected
> show #!1 models
> hide #!1 models
> select subtract #9/C:464
45 atoms, 49 bonds, 2 residues, 1 model selected
> show #!1 models
> hide #!1 models
> select subtract #9/C:465
23 atoms, 25 bonds, 1 residue, 1 model selected
> show #!1 models
> hide #!1 models
> select add #9/C:465
45 atoms, 49 bonds, 2 residues, 1 model selected
> select add #9/C:464
67 atoms, 73 bonds, 3 residues, 1 model selected
> show #!1 models
> select clear
> hide #!9 models
> hide #!1 models
> show #7 models
> hide #7 models
> show #!4 models
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/fold_r_e/fold_r_e_model_0.cif
Chain information for fold_r_e_model_0.cif #10
---
Chain | Description
A | .
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/fold_r_e/fold_r_e_model_1.cif
Chain information for fold_r_e_model_1.cif #11
---
Chain | Description
A | .
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/fold_r_e/fold_r_e_model_2.cif
Chain information for fold_r_e_model_2.cif #12
---
Chain | Description
A | .
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/fold_r_e/fold_r_e_model_3.cif
Chain information for fold_r_e_model_3.cif #13
---
Chain | Description
A | .
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/fold_r_e/fold_r_e_model_4.cif
Chain information for fold_r_e_model_4.cif #14
---
Chain | Description
A | .
> 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 #15
---
Chain | Description
B | .
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/fold_r_e_m/fold_r_e_m_model_1.cif
Chain information for fold_r_e_m_model_1.cif #16
---
Chain | Description
B | .
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/fold_r_e_m/fold_r_e_m_model_2.cif
Chain information for fold_r_e_m_model_2.cif #17
---
Chain | Description
B | .
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/fold_r_e_m/fold_r_e_m_model_3.cif
Chain information for fold_r_e_m_model_3.cif #18
---
Chain | Description
B | .
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/fold_r_e_m/fold_r_e_m_model_4.cif
Chain information for fold_r_e_m_model_4.cif #19
---
Chain | Description
B | .
> hide #!4 models
> hide #11 models
> hide #12 models
> hide #13 models
> hide #14 models
> hide #15 models
> hide #16 models
> hide #17 models
> hide #18 models
> hide #19 models
> show #11 models
> hide #10 models
> show #12 models
> hide #11 models
> hide #12 models
> show #13 models
> show #14 models
> hide #13 models
> show #15 models
> hide #14 models
> close #15
> show #16 models
> show #!3 models
> hide #16 models
> show #14 models
> hide #!3 models
> show #16 models
> hide #14 models
> show #!3 models
> hide #!3 models
> show #17 models
> hide #16 models
> show #18 models
> hide #17 models
> hide #18 models
> show #19 models
> show #!4 models
> hide #19 models
> hide #!4 models
> show #!1 models
> close #3
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-combine-new-5-coot-0.pdb
Chain information for R-combine-new-5-coot-0.pdb #3
---
Chain | Description
A C E | No description available
B | No description available
H | No description available
> show #!2 models
> hide #!1 models
> select #3/E:399@C1'
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,15.391,0,1,0,-111.14,0,0,1,2.6748
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.43036,0.79861,0.42074,-25.796,0.054189,0.48812,-0.87109,254.25,-0.90103,-0.35208,-0.25334,622.74
> view matrix models
> #3,0.067834,0.54249,-0.83732,239.04,0.81557,-0.51356,-0.26666,281.75,-0.57468,-0.6648,-0.47727,706.62
> view matrix models
> #3,0.30377,0.95269,-0.010786,-148.17,0.95167,-0.30287,0.050895,104.26,0.045221,-0.025725,-0.99865,465.06
> view matrix models
> #3,-0.59391,0.77108,-0.22958,172.43,0.80402,0.55864,-0.20366,-98.201,-0.028787,-0.30554,-0.95174,567.31
> view matrix models
> #3,-0.39636,0.78991,-0.46791,175.64,0.91488,0.38246,-0.12933,-80.613,0.076801,-0.47934,-0.87426,584.57
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.39636,0.78991,-0.46791,144.59,0.91488,0.38246,-0.12933,-84.708,0.076801,-0.47934,-0.87426,581.86
> view matrix models
> #3,-0.39636,0.78991,-0.46791,141.24,0.91488,0.38246,-0.12933,-111.63,0.076801,-0.47934,-0.87426,550.16
> view matrix models
> #3,-0.39636,0.78991,-0.46791,135.36,0.91488,0.38246,-0.12933,-119.33,0.076801,-0.47934,-0.87426,550.93
> fitmap #3 inMap #2
Fit molecule R-combine-new-5-coot-0.pdb (#3) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 11436 atoms
average map value = 4.709, steps = 188
shifted from previous position = 5.99
rotated from previous position = 13 degrees
atoms outside contour = 5139, contour level = 3.0813
Position of R-combine-new-5-coot-0.pdb (#3) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
-0.41961369 0.64793245 -0.63569480 231.71962100
0.89959345 0.39025554 -0.19604141 -98.64878510
0.12106183 -0.65412854 -0.74663236 569.49521585
Axis -0.49808039 -0.82282520 0.27363224
Axis point 66.35267423 0.00000000 311.60398600
Rotation angle (degrees) 152.62240305
Shift along axis 121.58795967
> view matrix models
> #3,-0.41961,0.64793,-0.63569,236.19,0.89959,0.39026,-0.19604,-91.184,0.12106,-0.65413,-0.74663,572.17
> fitmap #3 inMap #2
Fit molecule R-combine-new-5-coot-0.pdb (#3) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 11436 atoms
average map value = 4.709, steps = 148
shifted from previous position = 9.1
rotated from previous position = 0.00329 degrees
atoms outside contour = 5140, contour level = 3.0813
Position of R-combine-new-5-coot-0.pdb (#3) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
-0.41962582 0.64789351 -0.63572649 231.74592504
0.89958812 0.39025211 -0.19607268 -98.64046689
0.12105939 -0.65416916 -0.74659717 569.50157828
Axis -0.49807002 -0.82282308 0.27365751
Axis point 66.35832087 0.00000000 311.61270117
Rotation angle (degrees) 152.62117954
Shift along axis 121.58633897
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
1104 atoms, 1237 bonds, 52 residues, 1 model selected
> select up
11436 atoms, 12808 bonds, 534 residues, 1 model selected
> style sel stick
Changed 11436 atom styles
> cartoon sel
> hide #!2 models
> hide #!3 models
> show #!4 models
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R_mid_2.pdb
Chain information for R_mid_2.pdb #15
---
Chain | Description
B | No description available
> show #!6 models
> close #15
> color #6 #ba5bdbff
> select #4/B:387
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #4/B:392
42 atoms, 45 bonds, 2 residues, 1 model selected
> select clear
Drag select of 43 residues, 82 shapes
> delete atoms sel
> delete bonds sel
Drag select of 8 residues, 1 pseudobonds, 17 shapes
> delete atoms (#!4 & sel)
> delete bonds (#!4 & sel)
> select add #4/B:413
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #4/B:414
43 atoms, 46 bonds, 2 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> delete atoms sel
> delete bonds sel
> show #!2 models
> select clear
> select #6/B:359
22 atoms, 24 bonds, 1 residue, 1 model selected
> view matrix models
> #6,0.82245,-0.4005,-0.40395,296.01,-0.38298,0.13521,-0.91381,357.11,0.4206,0.90626,-0.042185,271.28
> view matrix models
> #6,0.82245,-0.4005,-0.40395,173.15,-0.38298,0.13521,-0.91381,352.4,0.4206,0.90626,-0.042185,232.01
> view matrix models
> #6,0.82245,-0.4005,-0.40395,155.57,-0.38298,0.13521,-0.91381,224.72,0.4206,0.90626,-0.042185,138.61
> view matrix models
> #6,0.82245,-0.4005,-0.40395,196.28,-0.38298,0.13521,-0.91381,253.93,0.4206,0.90626,-0.042185,216.46
> view matrix models
> #6,0.82245,-0.4005,-0.40395,196.09,-0.38298,0.13521,-0.91381,215.85,0.4206,0.90626,-0.042185,227.29
> view matrix models
> #6,0.82245,-0.4005,-0.40395,175.78,-0.38298,0.13521,-0.91381,188.2,0.4206,0.90626,-0.042185,246.49
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.3642,-0.55537,-0.74761,168.37,-0.8995,-0.41781,-0.12781,192.13,-0.24138,0.71902,-0.65172,234.76
> view matrix models
> #6,0.49153,-0.6895,-0.53197,170.11,-0.86805,-0.33883,-0.36289,189.83,0.069965,0.64014,-0.76506,232.93
> view matrix models
> #6,0.26057,-0.59304,-0.76184,167.57,-0.94872,-0.010993,-0.31593,193.94,0.17898,0.80509,-0.5655,237.73
> view matrix models
> #6,0.051678,-0.72074,-0.69128,166.74,-0.98605,0.072853,-0.14967,197.04,0.15824,0.68937,-0.70692,234.5
> view matrix models
> #6,0.0050157,-0.89416,-0.44772,168.03,-0.93875,0.15007,-0.31022,195.81,0.34457,0.42185,-0.83864,230.08
> view matrix models
> #6,0.38346,-0.89225,-0.23845,171.65,-0.7058,-0.11659,-0.69875,188.19,0.59566,0.43624,-0.67446,232.97
> view matrix models
> #6,0.39317,-0.76948,-0.50331,169.39,-0.87838,-0.15254,-0.45296,190.79,0.27177,0.62019,-0.73588,233.44
> view matrix models
> #6,0.2487,-0.8659,-0.43401,168.98,-0.9146,-0.062445,-0.39951,192.42,0.31883,0.49631,-0.80748,231.22
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.2487,-0.8659,-0.43401,171.05,-0.9146,-0.062445,-0.39951,204.18,0.31883,0.49631,-0.80748,239.79
> view matrix models
> #6,0.2487,-0.8659,-0.43401,185.2,-0.9146,-0.062445,-0.39951,199.52,0.31883,0.49631,-0.80748,246.18
> view matrix models
> #6,0.2487,-0.8659,-0.43401,184.42,-0.9146,-0.062445,-0.39951,194.83,0.31883,0.49631,-0.80748,246.36
> fitmap #6 inMap #2
Fit molecule R_mid_2.pdb (#6) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 706 atoms
average map value = 4.789, steps = 160
shifted from previous position = 3.25
rotated from previous position = 45.4 degrees
atoms outside contour = 276, contour level = 3.0813
Position of R_mid_2.pdb (#6) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
-0.18583593 -0.59079798 -0.78512595 179.71240486
-0.96931860 -0.02060986 0.24494221 204.59048513
-0.16089270 0.80655625 -0.56884142 253.34117726
Axis 0.60974613 -0.67773201 -0.41096103
Axis point 146.14279044 0.00000000 111.60540170
Rotation angle (degrees) 152.57862036
Shift along axis -133.19192918
> show #!3 models
> select #6/B:423
20 atoms, 21 bonds, 1 residue, 1 model selected
> view matrix models
> #6,-0.18584,-0.5908,-0.78513,180.29,-0.96932,-0.02061,0.24494,204.22,-0.16089,0.80656,-0.56884,249.19
> view matrix models
> #6,-0.18584,-0.5908,-0.78513,181.98,-0.96932,-0.02061,0.24494,206.79,-0.16089,0.80656,-0.56884,248.94
> view matrix models
> #6,-0.18584,-0.5908,-0.78513,182.38,-0.96932,-0.02061,0.24494,205.43,-0.16089,0.80656,-0.56884,248.54
> fitmap #6 inMap #2
Fit molecule R_mid_2.pdb (#6) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 706 atoms
average map value = 5.655, steps = 116
shifted from previous position = 4
rotated from previous position = 28.8 degrees
atoms outside contour = 232, contour level = 3.0813
Position of R_mid_2.pdb (#6) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
-0.57000016 -0.34097102 -0.74755507 184.43354957
-0.79142302 -0.01664767 0.61104211 212.46599963
-0.22079270 0.93992639 -0.26036314 257.45055643
Axis 0.42869781 -0.68663018 -0.58716028
Axis point 139.74382600 0.00000000 78.23504452
Rotation angle (degrees) 157.44406321
Shift along axis -217.98404753
> hide #!2 models
> select clear
Drag select of 567 residues, 4 pseudobonds, 99 shapes, 8231 atoms, 9076 bonds
> combine #3 #6
Remapping chain ID 'B' in R_mid_2.pdb #6 to 'D'
> hide #!6 models
> hide #!3 models
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-combine-new-6.pdb models #4
> relModel #4
> select #4/C:466
23 atoms, 25 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected atoms"
> select #4/C:465
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #4/C:466
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #4/C:461
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #4/C:462
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #4/C:463
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #4/C:464
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #4/C:465
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #4/C:466
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #4/C:459
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #4/C:460
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #4/C:461
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #4/C:462
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #4/C:463
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #4/C:465
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #4/C:466
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #4/C:467
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #4/C:466
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #4/C:465
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #4/C:464
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #4/C:463
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #4/C:465
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #4/C:466
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #4/C:464
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #4/C:463
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #4/C:465
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #4/C:466
23 atoms, 25 bonds, 1 residue, 1 model selected
> select clear
> select #4/D:418
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #4/D:417
44 atoms, 48 bonds, 2 residues, 1 model selected
> select add #4/D:416
67 atoms, 73 bonds, 3 residues, 1 model selected
> select add #4/D:415
87 atoms, 94 bonds, 4 residues, 1 model selected
> select subtract #4/D:418
65 atoms, 70 bonds, 3 residues, 1 model selected
> select add #4/D:418
87 atoms, 94 bonds, 4 residues, 1 model selected
> select subtract #4/D:417
65 atoms, 70 bonds, 3 residues, 1 model selected
> select subtract #4/D:418
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add #4/D:417
65 atoms, 70 bonds, 3 residues, 1 model selected
> select subtract #4/D:417
43 atoms, 45 bonds, 2 residues, 1 model selected
> select subtract #4/D:415
23 atoms, 24 bonds, 1 residue, 1 model selected
> select add #4/D:415
43 atoms, 45 bonds, 2 residues, 1 model selected
> select subtract #4/D:416
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #4/D:418
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add #4/D:417
64 atoms, 69 bonds, 3 residues, 1 model selected
> select add #4/D:416
87 atoms, 94 bonds, 4 residues, 1 model selected
> select subtract #4/D:415
67 atoms, 73 bonds, 3 residues, 1 model selected
> select subtract #4/D:416
44 atoms, 48 bonds, 2 residues, 1 model selected
> select subtract #4/D:417
22 atoms, 24 bonds, 1 residue, 1 model selected
> select subtract #4/D:418
Nothing selected
> select add #4/D:417
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #4/D:416
45 atoms, 49 bonds, 2 residues, 1 model selected
> select add #4/D:415
65 atoms, 70 bonds, 3 residues, 1 model selected
> select clear
> select add #4/D:415
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #4/D:416
43 atoms, 46 bonds, 2 residues, 1 model selected
> select subtract #4/D:415
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #4/D:415
43 atoms, 46 bonds, 2 residues, 1 model selected
> select subtract #4/D:416
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #4/D:418
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add #4/D:417
64 atoms, 69 bonds, 3 residues, 1 model selected
> select clear
> select #4/D:417
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #4/D:416
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #4/D:415
20 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
> select add #4/D:417
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #4/D:418
44 atoms, 48 bonds, 2 residues, 1 model selected
> select add #4/D:415
64 atoms, 69 bonds, 3 residues, 1 model selected
> select add #4/D:416
87 atoms, 94 bonds, 4 residues, 1 model selected
> select subtract #4/D:418
65 atoms, 70 bonds, 3 residues, 1 model selected
> select subtract #4/D:417
43 atoms, 46 bonds, 2 residues, 1 model selected
> select subtract #4/D:416
20 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-combine-new-6_1.pdb models
> #4 relModel #4
> select #4/C:333
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #4/C:330
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #4/C:329
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #4/C:330
20 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
> show #!1 models
> hide #!1 models
> show #!2 models
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-combine-new-6_1.pdb models
> #4 relModel #2
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/RealSpaceRefine_5/R-combine-
> new-6_1_real_space_refined_005.pdb
Chain information for R-combine-new-6_1_real_space_refined_005.pdb #15
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
H | No description available
> select #15/H:577@C2'
1 atom, 1 residue, 1 model selected
> select up
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
6069 atoms, 6800 bonds, 283 residues, 1 model selected
> select up
12142 atoms, 13596 bonds, 567 residues, 1 model selected
> style sel stick
Changed 12142 atom styles
> cartoon sel
> hide #!4 models
> show #!3 models
> hide #!3 models
> close #15
> show #10 models
> show #11 models
> hide #10 models
> hide #11 models
> show #16 models
> 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 #15
---
Chain | Description
B | .
> hide #!2 models
> hide #16 models
> show #16 models
> hide #15 models
> select #16/B:358
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #16/B:359
44 atoms, 48 bonds, 2 residues, 1 model selected
> select add #16/B:360
67 atoms, 73 bonds, 3 residues, 1 model selected
> select add #16/B:361
87 atoms, 94 bonds, 4 residues, 1 model selected
> select add #16/B:362
107 atoms, 115 bonds, 5 residues, 1 model selected
> select add #16/B:363
129 atoms, 139 bonds, 6 residues, 1 model selected
> select add #16/B:364
152 atoms, 164 bonds, 7 residues, 1 model selected
> select add #16/B:365
172 atoms, 185 bonds, 8 residues, 1 model selected
> select add #16/B:366
192 atoms, 206 bonds, 9 residues, 1 model selected
> select add #16/B:367
212 atoms, 227 bonds, 10 residues, 1 model selected
> select add #16/B:368
234 atoms, 251 bonds, 11 residues, 1 model selected
> select add #16/B:417
256 atoms, 275 bonds, 12 residues, 1 model selected
> select add #16/B:416
279 atoms, 300 bonds, 13 residues, 1 model selected
> select add #16/B:415
299 atoms, 321 bonds, 14 residues, 1 model selected
> select add #16/B:414
319 atoms, 342 bonds, 15 residues, 1 model selected
> select add #16/B:413
342 atoms, 367 bonds, 16 residues, 1 model selected
> select add #16/B:412
362 atoms, 388 bonds, 17 residues, 1 model selected
> select add #16/B:411
384 atoms, 412 bonds, 18 residues, 1 model selected
> select add #16/B:410
406 atoms, 436 bonds, 19 residues, 1 model selected
> select add #16/B:409
426 atoms, 457 bonds, 20 residues, 1 model selected
> select add #16/B:408
446 atoms, 478 bonds, 21 residues, 1 model selected
> select add #16/B:407
466 atoms, 499 bonds, 22 residues, 1 model selected
> select add #16/B:406
488 atoms, 523 bonds, 23 residues, 1 model selected
> select add #16/B:405
508 atoms, 544 bonds, 24 residues, 1 model selected
> select add #16/B:404
528 atoms, 565 bonds, 25 residues, 1 model selected
> select add #16/B:403
572 atoms, 589 bonds, 27 residues, 1 model selected
> select add #16/B:402
592 atoms, 610 bonds, 28 residues, 1 model selected
> select add #16/B:376
612 atoms, 631 bonds, 29 residues, 1 model selected
> select add #16/B:375
634 atoms, 655 bonds, 30 residues, 1 model selected
> select add #16/B:373
656 atoms, 679 bonds, 31 residues, 1 model selected
> select add #16/B:374
676 atoms, 700 bonds, 32 residues, 1 model selected
> select add #16/B:372
698 atoms, 724 bonds, 33 residues, 1 model selected
> select add #16/B:370
720 atoms, 748 bonds, 34 residues, 1 model selected
> select add #16/B:371
742 atoms, 772 bonds, 35 residues, 1 model selected
> select add #16/B:369
762 atoms, 793 bonds, 36 residues, 1 model selected
> select add #16/B:401
784 atoms, 817 bonds, 37 residues, 1 model selected
> select add #16/B:400
806 atoms, 841 bonds, 38 residues, 1 model selected
> select add #16/B:399
826 atoms, 862 bonds, 39 residues, 1 model selected
> select add #16/B:398
848 atoms, 886 bonds, 40 residues, 1 model selected
> select add #16/B:397
870 atoms, 910 bonds, 41 residues, 1 model selected
> select add #16/B:396
890 atoms, 931 bonds, 42 residues, 1 model selected
> select add #16/B:395
912 atoms, 955 bonds, 43 residues, 1 model selected
> select add #16/B:394
932 atoms, 976 bonds, 44 residues, 1 model selected
> select add #16/B:378
952 atoms, 997 bonds, 45 residues, 1 model selected
> select add #16/B:379
975 atoms, 1022 bonds, 46 residues, 1 model selected
> select add #16/B:380
997 atoms, 1046 bonds, 47 residues, 1 model selected
> select add #16/B:381
1017 atoms, 1067 bonds, 48 residues, 1 model selected
> select add #16/B:382
1039 atoms, 1091 bonds, 49 residues, 1 model selected
> select add #16/B:383
1059 atoms, 1112 bonds, 50 residues, 1 model selected
> select add #16/B:384
1081 atoms, 1136 bonds, 51 residues, 1 model selected
> select add #16/B:385
1103 atoms, 1160 bonds, 52 residues, 1 model selected
> select add #16/B:386
1126 atoms, 1185 bonds, 53 residues, 1 model selected
> select add #16/B:387
1148 atoms, 1209 bonds, 54 residues, 1 model selected
> select add #16/B:388
1170 atoms, 1233 bonds, 55 residues, 1 model selected
> select add #16/B:389
1192 atoms, 1257 bonds, 56 residues, 1 model selected
> select add #16/B:390
1214 atoms, 1281 bonds, 57 residues, 1 model selected
> select add #16/B:391
1236 atoms, 1305 bonds, 58 residues, 1 model selected
> select add #16/B:392
1256 atoms, 1326 bonds, 59 residues, 1 model selected
> select add #16/B:393
1276 atoms, 1347 bonds, 60 residues, 1 model selected
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-combine-new-6_1-coot-0.pdb
Chain information for R-combine-new-6_1-coot-0.pdb #20
---
Chain | Description
A | No description available
B | No description available
C | No description available
E | No description available
H | No description available
> select add #16/B:43
1298 atoms, 1371 bonds, 61 residues, 1 model selected
> select add #16/B:44
1320 atoms, 1395 bonds, 62 residues, 1 model selected
> select add #16/B:45
1340 atoms, 1416 bonds, 63 residues, 1 model selected
> select add #16/B:46
1362 atoms, 1440 bonds, 64 residues, 1 model selected
> select add #16/B:47
1385 atoms, 1465 bonds, 65 residues, 1 model selected
> select add #16/B:418
1407 atoms, 1489 bonds, 66 residues, 1 model selected
> select add #16/B:419
1427 atoms, 1510 bonds, 67 residues, 1 model selected
> select add #16/B:420
1450 atoms, 1535 bonds, 68 residues, 1 model selected
> select add #16/B:421
1470 atoms, 1556 bonds, 69 residues, 1 model selected
> select add #16/B:422
1490 atoms, 1577 bonds, 70 residues, 1 model selected
> select add #16/B:423
1510 atoms, 1598 bonds, 71 residues, 1 model selected
> select add #16/B:357
1530 atoms, 1619 bonds, 72 residues, 1 model selected
> select add #16/B:42
1553 atoms, 1644 bonds, 73 residues, 1 model selected
> select add #16/B:41
1573 atoms, 1665 bonds, 74 residues, 1 model selected
> select add #16/B:526
1596 atoms, 1690 bonds, 75 residues, 1 model selected
> select subtract #16/B:526
1573 atoms, 1665 bonds, 74 residues, 1 model selected
> select add #16/B:40
1593 atoms, 1686 bonds, 75 residues, 1 model selected
> select add #16/B:39
1613 atoms, 1707 bonds, 76 residues, 1 model selected
> select add #16/B:37
1635 atoms, 1731 bonds, 77 residues, 1 model selected
> select add #16/B:38
1658 atoms, 1756 bonds, 78 residues, 1 model selected
> select add #16/B:36
1680 atoms, 1780 bonds, 79 residues, 1 model selected
> select add #16/B:48
1700 atoms, 1801 bonds, 80 residues, 1 model selected
> select ~sel & ##selected
10646 atoms, 11929 bonds, 498 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!1 models
> show #!2 models
> select #16/B:415
20 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> ui mousemode right "translate selected atoms"
> ui mousemode right "translate selected models"
> view matrix models #16,1,0,0,145.93,0,1,0,288.33,0,0,1,411.12
> view matrix models #16,1,0,0,318.89,0,1,0,157.22,0,0,1,170.31
> hide #!1 models
> view matrix models #16,1,0,0,221.04,0,1,0,149.26,0,0,1,306.12
> view matrix models #16,1,0,0,146.32,0,1,0,167.13,0,0,1,302.3
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.80202,0.27094,-0.53231,211.85,-0.16662,0.75434,0.63499,167.16,0.57359,0.59797,-0.55985,296.69
> view matrix models
> #16,-0.98486,-0.013981,-0.17279,216.23,-0.13081,0.71399,0.68782,165.66,0.11375,0.70001,-0.70501,313.18
> view matrix models
> #16,-0.72042,0.27584,-0.63633,210.35,-0.56011,0.30965,0.76837,182.77,0.40899,0.90996,-0.068574,293.65
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.72042,0.27584,-0.63633,178.55,-0.56011,0.30965,0.76837,201.4,0.40899,0.90996,-0.068574,265.67
> view matrix models
> #16,-0.72042,0.27584,-0.63633,185.77,-0.56011,0.30965,0.76837,194.79,0.40899,0.90996,-0.068574,253.45
> select #20/C:485@P
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
3410 atoms, 3813 bonds, 160 residues, 1 model selected
> select up
11519 atoms, 12901 bonds, 538 residues, 1 model selected
> style sel stick
Changed 11519 atom styles
> cartoon sel
> select clear
> select #16/B:36
22 atoms, 24 bonds, 1 residue, 1 model selected
> view matrix models
> #16,-0.72042,0.27584,-0.63633,179.91,-0.56011,0.30965,0.76837,164.71,0.40899,0.90996,-0.068574,253.79
> select #20/E:358
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #20/E:359
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add #20/E:360
63 atoms, 67 bonds, 3 residues, 1 model selected
> select add #20/E:361
85 atoms, 91 bonds, 4 residues, 1 model selected
> select add #20/E:362
108 atoms, 116 bonds, 5 residues, 1 model selected
> select add #20/E:363
128 atoms, 137 bonds, 6 residues, 1 model selected
> select add #20/E:364
148 atoms, 158 bonds, 7 residues, 1 model selected
> select add #20/E:365
168 atoms, 179 bonds, 8 residues, 1 model selected
> select add #20/E:366
190 atoms, 204 bonds, 9 residues, 1 model selected
> select add #20/E:367
210 atoms, 225 bonds, 10 residues, 1 model selected
> select add #20/E:368
232 atoms, 249 bonds, 11 residues, 1 model selected
> select add #20/E:369
254 atoms, 273 bonds, 12 residues, 1 model selected
> select #16/B:414
20 atoms, 21 bonds, 1 residue, 1 model selected
> view matrix models
> #16,-0.72042,0.27584,-0.63633,206.93,-0.56011,0.30965,0.76837,195.1,0.40899,0.90996,-0.068574,234.04
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.79718,0.53246,-0.28459,203.04,0.0074598,0.48002,0.87723,173.07,0.6037,0.69718,-0.38664,233.13
> view matrix models
> #16,-0.81382,0.5389,-0.21745,202.74,0.024547,0.40574,0.91366,172.7,0.5806,0.73822,-0.34343,233.03
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.81382,0.5389,-0.21745,202.66,0.024547,0.40574,0.91366,180.32,0.5806,0.73822,-0.34343,234.73
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.88022,0.38759,-0.27385,206.88,-0.069757,0.46512,0.8825,183.38,0.46942,0.79589,-0.38237,238.5
> view matrix models
> #16,-0.82168,0.45251,-0.34654,205.09,-0.26648,0.23246,0.93539,191.43,0.50382,0.86093,-0.07042,233
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.82168,0.45251,-0.34654,206.49,-0.26648,0.23246,0.93539,191.41,0.50382,0.86093,-0.07042,231.86
> hide #!2 models
> hide #!20 models
> show #!20 models
> view matrix models
> #16,-0.82168,0.45251,-0.34654,191.23,-0.26648,0.23246,0.93539,182.42,0.50382,0.86093,-0.07042,263.73
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.71954,0.64403,-0.25978,185.05,-0.29819,0.051298,0.95313,184.85,0.62717,0.76328,0.15513,257.68
> view matrix models
> #16,-0.64375,0.48676,-0.59046,187.82,-0.76507,-0.39372,0.50956,209.7,0.015554,0.77978,0.62586,272.47
> view matrix models
> #16,-0.57243,0.46953,-0.67221,186.52,-0.79572,-0.51595,0.31722,214.08,-0.19788,0.71647,0.66896,279.74
> view matrix models
> #16,-0.21945,0.53178,-0.81796,175.78,-0.48636,-0.78642,-0.38078,214.3,-0.84575,0.31426,0.43122,307.99
> view matrix models
> #16,-0.063723,0.61343,-0.78717,169.45,-0.1805,-0.78285,-0.59545,206.49,-0.98151,0.10414,0.16061,317.61
> view matrix models
> #16,-0.15428,0.56142,-0.81302,173.26,-0.37252,-0.7952,-0.47842,211.7,-0.91511,0.22905,0.33182,312.27
> view matrix models
> #16,-0.49855,0.46673,-0.73049,184.73,-0.78044,-0.60846,0.14388,216.43,-0.37732,0.64183,0.6676,286.52
> view matrix models
> #16,-0.29205,0.50526,-0.81205,178.38,-0.59285,-0.7619,-0.26084,216.26,-0.75049,0.40525,0.52205,302.94
> view matrix models
> #16,-0.25119,0.51937,-0.8168,176.94,-0.53545,-0.77754,-0.32974,215.28,-0.80635,0.35453,0.47341,305.84
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.25119,0.51937,-0.8168,184.35,-0.53545,-0.77754,-0.32974,210.7,-0.80635,0.35453,0.47341,282.43
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.12285,0.18387,-0.97524,184.73,-0.49826,-0.86129,-0.099622,207.36,-0.85828,0.47368,0.19743,286.53
> view matrix models
> #16,0.1038,-0.59594,-0.79629,181.63,-0.50066,-0.72309,0.47589,199.22,-0.8594,0.34927,-0.37343,294.63
> view matrix models
> #16,-0.73101,-0.18468,-0.65689,204.76,-0.29431,-0.7832,0.54771,191.89,-0.61563,0.59372,0.51817,273.55
> select clear
> ui mousemode right "translate selected models"
> select #16/B:366
20 atoms, 21 bonds, 1 residue, 1 model selected
> view matrix models
> #16,-0.73101,-0.18468,-0.65689,209.52,-0.29431,-0.7832,0.54771,194.23,-0.61563,0.59372,0.51817,270.19
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.49537,-0.088551,-0.86416,203.16,-0.23268,-0.94492,0.23021,197.38,-0.83694,0.31511,0.44748,281.01
> view matrix models
> #16,-0.52709,-0.10637,-0.84312,204.13,-0.24693,-0.93016,0.27172,197.23,-0.81314,0.35141,0.46402,279.69
> view matrix models
> #16,-0.22706,0.12978,-0.96519,193.38,-0.6193,-0.78412,0.040258,211.49,-0.7516,0.60689,0.25842,277.85
> view matrix models
> #16,-0.35294,0.11995,-0.92793,197.29,-0.67089,-0.72373,0.16162,211.25,-0.65219,0.67958,0.3359,272.9
> view matrix models
> #16,0.059853,0.19546,-0.97888,183.25,-0.42658,-0.88158,-0.20211,208.74,-0.90247,0.42967,0.030615,287.26
> ui mousemode right "translate selected models"
> view matrix models
> #16,0.059853,0.19546,-0.97888,200.7,-0.42658,-0.88158,-0.20211,209.03,-0.90247,0.42967,0.030615,266.57
> ui mousemode right "rotate selected models"
> view matrix models
> #16,0.23054,-0.13974,-0.96298,197.6,-0.47739,-0.87859,0.013207,208.08,-0.84791,0.45667,-0.26927,268.17
> view matrix models
> #16,0.3491,-0.065072,-0.93482,192.61,-0.72618,-0.64931,-0.22598,217.41,-0.59228,0.75774,-0.27392,257.02
> view matrix models
> #16,0.60451,-0.039885,-0.7956,182.13,-0.55119,-0.742,-0.3816,214.22,-0.57512,0.66921,-0.47053,259.59
> ui mousemode right "translate selected models"
> view matrix models
> #16,0.60451,-0.039885,-0.7956,192,-0.55119,-0.742,-0.3816,215.69,-0.57512,0.66921,-0.47053,255.91
> view matrix models
> #16,0.60451,-0.039885,-0.7956,200.34,-0.55119,-0.742,-0.3816,212.33,-0.57512,0.66921,-0.47053,258.77
> ui mousemode right "rotate selected models"
> view matrix models
> #16,0.62452,-0.29296,-0.72398,200.97,-0.62625,-0.74174,-0.24007,213.15,-0.46668,0.60332,-0.6467,257.8
> ui mousemode right "translate selected models"
> view matrix models
> #16,0.62452,-0.29296,-0.72398,195.72,-0.62625,-0.74174,-0.24007,211.64,-0.46668,0.60332,-0.6467,260.42
> ui mousemode right "rotate selected models"
> view matrix models
> #16,0.65269,-0.095449,-0.75159,193.42,-0.52007,-0.77783,-0.35285,209.73,-0.55093,0.62119,-0.55732,262.03
> view matrix models
> #16,0.65817,0.010853,-0.75279,192.34,-0.43781,-0.80792,-0.39443,207.72,-0.61248,0.58919,-0.527,264.01
> view matrix models
> #16,0.76096,-0.14884,-0.6315,188.71,-0.32675,-0.9288,-0.17482,202.34,-0.56052,0.33937,-0.75541,267.1
> view matrix models
> #16,0.75214,-0.037724,-0.65792,188.39,-0.31923,-0.89426,-0.31367,203.48,-0.57653,0.44595,-0.68465,265.88
> ui mousemode right "translate selected models"
> view matrix models
> #16,0.75214,-0.037724,-0.65792,193.71,-0.31923,-0.89426,-0.31367,203.7,-0.57653,0.44595,-0.68465,265.93
> view matrix models
> #16,0.75214,-0.037724,-0.65792,196.4,-0.31923,-0.89426,-0.31367,206.19,-0.57653,0.44595,-0.68465,266.73
> view matrix models
> #16,0.75214,-0.037724,-0.65792,197.82,-0.31923,-0.89426,-0.31367,208.24,-0.57653,0.44595,-0.68465,264.83
> view matrix models
> #16,0.75214,-0.037724,-0.65792,197.67,-0.31923,-0.89426,-0.31367,208.66,-0.57653,0.44595,-0.68465,264.63
> view matrix models
> #16,0.75214,-0.037724,-0.65792,195.17,-0.31923,-0.89426,-0.31367,208.71,-0.57653,0.44595,-0.68465,265.15
> view matrix models
> #16,0.75214,-0.037724,-0.65792,194.2,-0.31923,-0.89426,-0.31367,208.59,-0.57653,0.44595,-0.68465,265.25
> view matrix models
> #16,0.75214,-0.037724,-0.65792,194.64,-0.31923,-0.89426,-0.31367,209.44,-0.57653,0.44595,-0.68465,264.76
> show #!2 models
> hide #!16 models
> show #17 models
> hide #!2 models
> hide #!20 models
> view matrix models
> #16,0.75214,-0.037724,-0.65792,194.89,-0.31923,-0.89426,-0.31367,209.35,-0.57653,0.44595,-0.68465,264.46
> view matrix models
> #16,0.75214,-0.037724,-0.65792,156.47,-0.31923,-0.89426,-0.31367,236.83,-0.57653,0.44595,-0.68465,321.16
> show #18 models
> hide #17 models
> select #18/B:424
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #18/B:423
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add #18/B:422
62 atoms, 66 bonds, 3 residues, 1 model selected
> select add #18/B:421
82 atoms, 87 bonds, 4 residues, 1 model selected
> select add #18/B:420
105 atoms, 112 bonds, 5 residues, 1 model selected
> select add #18/B:419
125 atoms, 133 bonds, 6 residues, 1 model selected
> select add #18/B:418
147 atoms, 157 bonds, 7 residues, 1 model selected
> select add #18/B:45
167 atoms, 178 bonds, 8 residues, 1 model selected
> select add #18/B:46
189 atoms, 202 bonds, 9 residues, 1 model selected
> select add #18/B:48
209 atoms, 223 bonds, 10 residues, 1 model selected
> select add #18/B:47
232 atoms, 248 bonds, 11 residues, 1 model selected
> select add #18/B:44
254 atoms, 272 bonds, 12 residues, 1 model selected
> select add #18/B:43
276 atoms, 296 bonds, 13 residues, 1 model selected
> select add #18/B:42
299 atoms, 321 bonds, 14 residues, 1 model selected
> select add #18/B:41
319 atoms, 342 bonds, 15 residues, 1 model selected
> select add #18/B:40
339 atoms, 363 bonds, 16 residues, 1 model selected
> select add #18/B:39
359 atoms, 384 bonds, 17 residues, 1 model selected
> select add #18/B:38
382 atoms, 409 bonds, 18 residues, 1 model selected
> select add #18/B:37
404 atoms, 433 bonds, 19 residues, 1 model selected
> select add #18/B:36
426 atoms, 457 bonds, 20 residues, 1 model selected
> select add #18/B:356
446 atoms, 478 bonds, 21 residues, 1 model selected
> select add #18/B:357
466 atoms, 499 bonds, 22 residues, 1 model selected
> select add #18/B:358
488 atoms, 523 bonds, 23 residues, 1 model selected
> select add #18/B:359
510 atoms, 547 bonds, 24 residues, 1 model selected
> select add #18/B:360
533 atoms, 572 bonds, 25 residues, 1 model selected
> select add #18/B:417
555 atoms, 596 bonds, 26 residues, 1 model selected
> select add #18/B:416
578 atoms, 621 bonds, 27 residues, 1 model selected
> select add #18/B:414
598 atoms, 642 bonds, 28 residues, 1 model selected
> select add #18/B:415
618 atoms, 663 bonds, 29 residues, 1 model selected
> select add #18/B:413
641 atoms, 688 bonds, 30 residues, 1 model selected
> select add #18/B:412
661 atoms, 709 bonds, 31 residues, 1 model selected
> select add #18/B:361
681 atoms, 730 bonds, 32 residues, 1 model selected
> select add #18/B:362
701 atoms, 751 bonds, 33 residues, 1 model selected
> select add #18/B:363
723 atoms, 775 bonds, 34 residues, 1 model selected
> select add #18/B:364
746 atoms, 800 bonds, 35 residues, 1 model selected
> select add #18/B:365
766 atoms, 821 bonds, 36 residues, 1 model selected
> select add #18/B:366
786 atoms, 842 bonds, 37 residues, 1 model selected
> select add #18/B:367
806 atoms, 863 bonds, 38 residues, 1 model selected
> select add #18/B:368
828 atoms, 887 bonds, 39 residues, 1 model selected
> select add #18/B:369
848 atoms, 908 bonds, 40 residues, 1 model selected
> select add #18/B:370
870 atoms, 932 bonds, 41 residues, 1 model selected
> select add #18/B:371
892 atoms, 956 bonds, 42 residues, 1 model selected
> select add #18/B:411
914 atoms, 980 bonds, 43 residues, 1 model selected
> select add #18/B:410
936 atoms, 1004 bonds, 44 residues, 1 model selected
> select add #18/B:409
956 atoms, 1025 bonds, 45 residues, 1 model selected
> select add #18/B:408
976 atoms, 1046 bonds, 46 residues, 1 model selected
> select add #18/B:372
998 atoms, 1070 bonds, 47 residues, 1 model selected
> select add #18/B:373
1020 atoms, 1094 bonds, 48 residues, 1 model selected
> select add #18/B:407
1040 atoms, 1115 bonds, 49 residues, 1 model selected
> select add #18/B:406
1062 atoms, 1139 bonds, 50 residues, 1 model selected
> select add #18/B:405
1082 atoms, 1160 bonds, 51 residues, 1 model selected
> select add #18/B:404
1102 atoms, 1181 bonds, 52 residues, 1 model selected
> select add #18/B:403
1124 atoms, 1205 bonds, 53 residues, 1 model selected
> select add #18/B:402
1144 atoms, 1226 bonds, 54 residues, 1 model selected
> select add #18/B:374
1164 atoms, 1247 bonds, 55 residues, 1 model selected
> select add #18/B:375
1186 atoms, 1271 bonds, 56 residues, 1 model selected
> select add #18/B:401
1208 atoms, 1295 bonds, 57 residues, 1 model selected
> select add #18/B:400
1230 atoms, 1319 bonds, 58 residues, 1 model selected
> select add #18/B:399
1250 atoms, 1340 bonds, 59 residues, 1 model selected
> select add #18/B:398
1272 atoms, 1364 bonds, 60 residues, 1 model selected
> select add #18/B:397
1294 atoms, 1388 bonds, 61 residues, 1 model selected
> select add #18/B:396
1314 atoms, 1409 bonds, 62 residues, 1 model selected
> select add #18/B:395
1336 atoms, 1433 bonds, 63 residues, 1 model selected
> select add #18/B:394
1356 atoms, 1454 bonds, 64 residues, 1 model selected
> select add #18/B:393
1376 atoms, 1475 bonds, 65 residues, 1 model selected
> select add #18/B:392
1396 atoms, 1496 bonds, 66 residues, 1 model selected
> select add #18/B:391
1418 atoms, 1520 bonds, 67 residues, 1 model selected
> select add #18/B:390
1440 atoms, 1544 bonds, 68 residues, 1 model selected
> select add #18/B:389
1462 atoms, 1568 bonds, 69 residues, 1 model selected
> select add #18/B:388
1484 atoms, 1592 bonds, 70 residues, 1 model selected
> select add #18/B:387
1506 atoms, 1616 bonds, 71 residues, 1 model selected
> select add #18/B:386
1529 atoms, 1641 bonds, 72 residues, 1 model selected
> select add #18/B:385
1551 atoms, 1665 bonds, 73 residues, 1 model selected
> select add #18/B:384
1573 atoms, 1689 bonds, 74 residues, 1 model selected
> select add #18/B:383
1593 atoms, 1710 bonds, 75 residues, 1 model selected
> select add #18/B:376
1613 atoms, 1731 bonds, 76 residues, 1 model selected
> select add #18/B:377
1635 atoms, 1755 bonds, 77 residues, 1 model selected
> select add #18/B:378
1655 atoms, 1776 bonds, 78 residues, 1 model selected
> select add #18/B:379
1678 atoms, 1801 bonds, 79 residues, 1 model selected
> select add #18/B:380
1700 atoms, 1825 bonds, 80 residues, 1 model selected
> select add #18/B:381
1720 atoms, 1846 bonds, 81 residues, 1 model selected
> select add #18/B:382
1742 atoms, 1870 bonds, 82 residues, 1 model selected
> select ~sel & ##selected
10604 atoms, 11882 bonds, 496 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!2 models
> select clear
> select #18/B:400
22 atoms, 24 bonds, 1 residue, 1 model selected
> view matrix models #18,1,0,0,124.31,0,1,0,265.85,0,0,1,143.7
> view matrix models #18,1,0,0,190.29,0,1,0,218.77,0,0,1,254.31
> show #!20 models
> view matrix models #18,1,0,0,185.02,0,1,0,212.5,0,0,1,259.12
> ui mousemode right "rotate selected models"
> view matrix models
> #18,0.96094,0.22241,-0.16471,196.92,-0.22068,0.97492,0.028967,208.21,0.16702,0.0085143,0.98592,261.75
> view matrix models
> #18,0.88625,-0.029786,-0.46224,198.04,-0.24394,0.81832,-0.52043,221.09,0.39376,0.57399,0.71797,290.48
> view matrix models
> #18,0.228,0.7319,0.64213,178.44,0.26271,0.5888,-0.76439,227.65,-0.93755,0.34298,-0.058025,293.33
> view matrix models
> #18,-0.29655,0.42437,0.85555,156.08,0.32905,0.8864,-0.32562,223.41,-0.89654,0.18495,-0.4025,300.05
> view matrix models
> #18,-0.1019,0.1874,0.97698,147.08,0.69044,0.72036,-0.06616,214.06,-0.71618,0.66781,-0.2028,310.6
> view matrix models
> #18,-0.81192,0.077217,0.57864,148.28,0.47034,0.67366,0.57006,189.65,-0.34579,0.735,-0.58327,329.15
> view matrix models
> #18,-0.83525,0.21539,0.50593,154.68,0.44357,0.80769,0.38844,199.38,-0.32497,0.54886,-0.77016,329.59
> ui mousemode right "translate selected models"
> view matrix models
> #18,-0.83525,0.21539,0.50593,178.73,0.44357,0.80769,0.38844,212.38,-0.32497,0.54886,-0.77016,270.7
> view matrix models
> #18,-0.83525,0.21539,0.50593,181.22,0.44357,0.80769,0.38844,214.48,-0.32497,0.54886,-0.77016,266.51
> ui mousemode right "rotate selected models"
> view matrix models
> #18,0.049515,0.37543,0.92553,182.83,0.78182,0.56209,-0.26983,231.88,-0.62153,0.73696,-0.26568,252.72
> view matrix models
> #18,0.10358,0.53357,0.83939,191.12,0.82645,0.42338,-0.37111,231.44,-0.5534,0.73215,-0.39712,257.62
> ui mousemode right "translate selected models"
> view matrix models
> #18,0.10358,0.53357,0.83939,182.55,0.82645,0.42338,-0.37111,219.16,-0.5534,0.73215,-0.39712,259
> view matrix models
> #18,0.10358,0.53357,0.83939,198.62,0.82645,0.42338,-0.37111,218.04,-0.5534,0.73215,-0.39712,253.04
> view matrix models
> #18,0.10358,0.53357,0.83939,195.01,0.82645,0.42338,-0.37111,207.3,-0.5534,0.73215,-0.39712,260.67
> view matrix models
> #18,0.10358,0.53357,0.83939,197.94,0.82645,0.42338,-0.37111,208.89,-0.5534,0.73215,-0.39712,262.44
> ui mousemode right "rotate selected models"
> view matrix models
> #18,0.13436,0.45782,0.87883,194.68,0.75938,0.52219,-0.38814,211.72,-0.63662,0.71952,-0.2775,257.21
> ui mousemode right "translate selected models"
> view matrix models
> #18,0.13436,0.45782,0.87883,195.27,0.75938,0.52219,-0.38814,213.61,-0.63662,0.71952,-0.2775,260.73
> view matrix models
> #18,0.13436,0.45782,0.87883,198.54,0.75938,0.52219,-0.38814,211.47,-0.63662,0.71952,-0.2775,258.44
> view matrix models
> #18,0.13436,0.45782,0.87883,197.29,0.75938,0.52219,-0.38814,208.55,-0.63662,0.71952,-0.2775,260.21
> ui mousemode right "rotate selected models"
> view matrix models
> #18,0.032304,0.58865,0.80774,202.47,0.75986,0.51054,-0.40245,208.67,-0.64929,0.62677,-0.4308,262.22
> view matrix models
> #18,0.11879,0.64558,0.7544,206.93,0.64539,0.52719,-0.55277,212.75,-0.75456,0.55254,-0.35402,256.25
> ui mousemode right "translate selected models"
> view matrix models
> #18,0.11879,0.64558,0.7544,202.2,0.64539,0.52719,-0.55277,209.14,-0.75456,0.55254,-0.35402,262.54
> view matrix models
> #18,0.11879,0.64558,0.7544,200.53,0.64539,0.52719,-0.55277,210.65,-0.75456,0.55254,-0.35402,263.26
> view matrix models
> #18,0.11879,0.64558,0.7544,199.91,0.64539,0.52719,-0.55277,211.86,-0.75456,0.55254,-0.35402,262.62
> view matrix models
> #18,0.11879,0.64558,0.7544,199.68,0.64539,0.52719,-0.55277,211.62,-0.75456,0.55254,-0.35402,262.43
> view matrix models
> #18,0.11879,0.64558,0.7544,198.9,0.64539,0.52719,-0.55277,212.77,-0.75456,0.55254,-0.35402,263.97
> ui mousemode right "rotate selected models"
> view matrix models
> #18,0.2436,0.53222,0.8108,195.01,0.48299,0.65838,-0.57728,215.75,-0.84106,0.53223,-0.096678,254.03
> ui mousemode right "translate selected models"
> view matrix models
> #18,0.2436,0.53222,0.8108,194.55,0.48299,0.65838,-0.57728,214.97,-0.84106,0.53223,-0.096678,253.78
> view matrix models
> #18,0.2436,0.53222,0.8108,192.97,0.48299,0.65838,-0.57728,211.9,-0.84106,0.53223,-0.096678,258.34
> view matrix models
> #18,0.2436,0.53222,0.8108,197.47,0.48299,0.65838,-0.57728,212.51,-0.84106,0.53223,-0.096678,255.99
> view matrix models
> #18,0.2436,0.53222,0.8108,196.99,0.48299,0.65838,-0.57728,209.8,-0.84106,0.53223,-0.096678,258.6
> view matrix models
> #18,0.2436,0.53222,0.8108,200.7,0.48299,0.65838,-0.57728,210.32,-0.84106,0.53223,-0.096678,258.79
> view matrix models
> #18,0.2436,0.53222,0.8108,200.75,0.48299,0.65838,-0.57728,210.33,-0.84106,0.53223,-0.096678,258.76
> view matrix models
> #18,0.2436,0.53222,0.8108,200.36,0.48299,0.65838,-0.57728,209.81,-0.84106,0.53223,-0.096678,258.96
> select #20/E:358
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #20/E:359
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add #20/E:360
63 atoms, 67 bonds, 3 residues, 1 model selected
> select clear
> select add #20/E:358
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #20/E:359
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add #20/E:360
63 atoms, 67 bonds, 3 residues, 1 model selected
> select add #20/E:361
85 atoms, 91 bonds, 4 residues, 1 model selected
> select add #20/E:362
108 atoms, 116 bonds, 5 residues, 1 model selected
> select add #20/E:363
128 atoms, 137 bonds, 6 residues, 1 model selected
Drag select of 269 atoms, 20 residues, 301 bonds
> delete atoms sel
> delete bonds sel
Drag select of 383 atoms, 9 residues, 38 pseudobonds, 132 bonds
> delete atoms (#!20 & sel)
> delete bonds (#!20 & sel)
Drag select of 2 cryosparc_P104_J81_mono_3dot25_map_emready.mrc , 129 atoms, 5
residues, 15 pseudobonds, 33 bonds
> select clear
Drag select of 108 atoms, 2 residues, 14 pseudobonds, 14 bonds
> delete atoms (#!20 & sel)
> delete bonds (#!20 & sel)
> select add #20/E:386
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #20/E:385
44 atoms, 48 bonds, 2 residues, 1 model selected
> select add #20/E:384
67 atoms, 73 bonds, 3 residues, 1 model selected
> select add #20/E:383
89 atoms, 97 bonds, 4 residues, 1 model selected
> select add #20/E:382
111 atoms, 121 bonds, 5 residues, 1 model selected
> select add #20/E:381
131 atoms, 142 bonds, 6 residues, 1 model selected
> select add #20/E:380
153 atoms, 166 bonds, 7 residues, 1 model selected
> select add #20/E:407
175 atoms, 190 bonds, 8 residues, 1 model selected
> select add #20/E:408
197 atoms, 214 bonds, 9 residues, 1 model selected
> select add #20/E:387
219 atoms, 238 bonds, 10 residues, 1 model selected
> select add #20/E:389
241 atoms, 262 bonds, 11 residues, 1 model selected
> select add #20/E:390
261 atoms, 283 bonds, 12 residues, 1 model selected
> select add #20/E:388
283 atoms, 307 bonds, 13 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 29 atoms, 4 pseudobonds, 2 bonds
> delete atoms (#!20 & sel)
> delete bonds (#!20 & sel)
> show #!1 models
> hide #!2 models
> hide #!1 models
> combine #20 #18
Remapping chain ID 'B' in fold_r_e_m_model_3.cif #18 to 'D'
> hide #!18 models
> hide #!20 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select add #21/C:418
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #21/C:417
44 atoms, 48 bonds, 2 residues, 1 model selected
> select add #21/C:416
66 atoms, 72 bonds, 3 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 6 atoms, 4 bonds
> delete atoms sel
> delete bonds sel
> select add #21/D:418
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #21/C:356
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add #21/C:357
62 atoms, 66 bonds, 3 residues, 1 model selected
> select subtract #21/C:356
42 atoms, 45 bonds, 2 residues, 1 model selected
> select subtract #21/C:357
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #21/D:358
44 atoms, 48 bonds, 2 residues, 1 model selected
> select #21/D:364
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #21/D:414
43 atoms, 46 bonds, 2 residues, 1 model selected
> show #!1 models
> view matrix models #21,1,0,0,-8.7693,0,1,0,-14.804,0,0,1,22.836
> ui mousemode right "rotate selected models"
> view matrix models
> #21,0.2543,0.94777,0.19251,-66.95,0.50727,0.038761,-0.86091,239.7,-0.82341,0.31659,-0.47092,453.9
> view matrix models
> #21,-0.68016,0.60352,-0.4161,321.44,-0.13466,-0.66083,-0.73835,474.14,-0.72059,-0.44616,0.53075,355.18
> view matrix models
> #21,-0.37511,0.92431,-0.070233,125,-0.85078,-0.37337,-0.36981,491.53,-0.36805,-0.078969,0.92645,129.66
> view matrix models
> #21,-0.65309,0.7552,0.056089,186.44,-0.70017,-0.57396,-0.42466,508.49,-0.28851,-0.31662,0.90361,161.27
> ui mousemode right "translate selected models"
> view matrix models
> #21,-0.65309,0.7552,0.056089,171.52,-0.70017,-0.57396,-0.42466,546.06,-0.28851,-0.31662,0.90361,145.58
> view matrix models
> #21,-0.65309,0.7552,0.056089,182.42,-0.70017,-0.57396,-0.42466,545.65,-0.28851,-0.31662,0.90361,176.43
> view matrix models
> #21,-0.65309,0.7552,0.056089,198.67,-0.70017,-0.57396,-0.42466,567.67,-0.28851,-0.31662,0.90361,154.57
> view matrix models
> #21,-0.65309,0.7552,0.056089,195.3,-0.70017,-0.57396,-0.42466,570.07,-0.28851,-0.31662,0.90361,157.05
> fitmap #21 inMap #1
Fit molecule combination (#21) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 12111 atoms
average map value = 2.076, steps = 228
shifted from previous position = 16.7
rotated from previous position = 23.1 degrees
atoms outside contour = 6624, contour level = 1.6178
Position of combination (#21) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.41434302 0.90305975 -0.11315015 164.51293952
-0.67684832 -0.38886612 -0.62502759 558.93801477
-0.60843752 -0.18239033 0.77235843 224.57161218
Axis 0.25826786 0.28898789 -0.92183714
Axis point 285.41367365 263.97381758 0.00000000
Rotation angle (degrees) 121.02589032
Shift along axis -3.00373258
> view matrix models
> #21,-0.41434,0.90306,-0.11315,159.45,-0.67685,-0.38887,-0.62503,563.41,-0.60844,-0.18239,0.77236,227
> ui mousemode right "rotate selected models"
> view matrix models
> #21,-0.22457,0.92092,-0.31856,160.95,-0.38652,-0.38427,-0.83841,548.1,-0.89452,-0.065158,0.44225,336.38
> view matrix models
> #21,0.034869,0.99889,0.031721,17.242,-0.54531,0.045616,-0.83699,502.8,-0.83751,0.011887,0.5463,288.08
> view matrix models
> #21,-0.10296,0.99107,-0.084696,72.449,-0.50476,-0.12543,-0.8541,529.09,-0.8571,-0.045187,0.51317,309.66
> ui mousemode right "translate selected models"
> view matrix models
> #21,-0.10296,0.99107,-0.084696,74.808,-0.50476,-0.12543,-0.8541,524.41,-0.8571,-0.045187,0.51317,312.53
> fitmap #21 inMap #1
Fit molecule combination (#21) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 12111 atoms
average map value = 3.563, steps = 236
shifted from previous position = 5.67
rotated from previous position = 27.3 degrees
atoms outside contour = 2995, contour level = 1.6178
Position of combination (#21) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.47563704 0.87194109 0.11613841 131.02755956
-0.61348298 -0.23419670 -0.75418203 541.89723455
-0.63040307 -0.42996585 0.64631364 312.99000130
Axis 0.19141461 0.44075206 -0.87698236
Axis point 271.95736979 307.65925241 0.00000000
Rotation angle (degrees) 122.12445172
Shift along axis -10.56379909
> select add #21/D:359
65 atoms, 70 bonds, 3 residues, 1 model selected
> select add #21/D:361
85 atoms, 91 bonds, 4 residues, 1 model selected
> select add #21/D:360
108 atoms, 116 bonds, 5 residues, 1 model selected
> select add #21/D:362
128 atoms, 137 bonds, 6 residues, 1 model selected
> select add #21/D:363
150 atoms, 161 bonds, 7 residues, 1 model selected
> select add #21/D:419
170 atoms, 182 bonds, 8 residues, 1 model selected
> select subtract #21/D:419
150 atoms, 161 bonds, 7 residues, 1 model selected
> select add #21/D:418
172 atoms, 185 bonds, 8 residues, 1 model selected
> select add #21/D:419
192 atoms, 206 bonds, 9 residues, 1 model selected
> select add #21/D:417
214 atoms, 230 bonds, 10 residues, 1 model selected
> select add #21/D:416
237 atoms, 255 bonds, 11 residues, 1 model selected
> hide #!1 models
> select add #21/D:415
257 atoms, 276 bonds, 12 residues, 1 model selected
> select add #21/D:365
277 atoms, 297 bonds, 13 residues, 1 model selected
> select add #21/D:366
297 atoms, 318 bonds, 14 residues, 1 model selected
> select add #21/D:413
320 atoms, 343 bonds, 15 residues, 1 model selected
> select add #21/D:412
340 atoms, 364 bonds, 16 residues, 1 model selected
> select add #21/D:411
362 atoms, 388 bonds, 17 residues, 1 model selected
> select add #21/D:410
384 atoms, 412 bonds, 18 residues, 1 model selected
> select add #21/D:409
404 atoms, 433 bonds, 19 residues, 1 model selected
> select add #21/D:408
424 atoms, 454 bonds, 20 residues, 1 model selected
> select add #21/D:367
444 atoms, 475 bonds, 21 residues, 1 model selected
> select add #21/D:368
466 atoms, 499 bonds, 22 residues, 1 model selected
> select add #21/D:369
486 atoms, 520 bonds, 23 residues, 1 model selected
> select add #21/D:370
508 atoms, 544 bonds, 24 residues, 1 model selected
> select add #21/D:371
530 atoms, 568 bonds, 25 residues, 1 model selected
> select add #21/D:407
550 atoms, 589 bonds, 26 residues, 1 model selected
> select add #21/D:406
572 atoms, 613 bonds, 27 residues, 1 model selected
> select add #21/D:372
594 atoms, 637 bonds, 28 residues, 1 model selected
> select add #21/D:373
616 atoms, 661 bonds, 29 residues, 1 model selected
> select add #21/D:374
636 atoms, 682 bonds, 30 residues, 1 model selected
> select add #21/D:375
658 atoms, 706 bonds, 31 residues, 1 model selected
> select add #21/D:405
678 atoms, 727 bonds, 32 residues, 1 model selected
> select add #21/D:404
698 atoms, 748 bonds, 33 residues, 1 model selected
> select add #21/D:403
720 atoms, 772 bonds, 34 residues, 1 model selected
> select add #21/D:402
740 atoms, 793 bonds, 35 residues, 1 model selected
> select add #21/D:401
762 atoms, 817 bonds, 36 residues, 1 model selected
> select add #21/D:400
784 atoms, 841 bonds, 37 residues, 1 model selected
> select add #21/D:399
804 atoms, 862 bonds, 38 residues, 1 model selected
> select add #21/D:398
826 atoms, 886 bonds, 39 residues, 1 model selected
> select add #21/D:397
848 atoms, 910 bonds, 40 residues, 1 model selected
> select add #21/D:396
868 atoms, 931 bonds, 41 residues, 1 model selected
> select add #21/D:376
888 atoms, 952 bonds, 42 residues, 1 model selected
> select add #21/D:377
910 atoms, 976 bonds, 43 residues, 1 model selected
> select add #21/D:378
930 atoms, 997 bonds, 44 residues, 1 model selected
> select add #21/D:379
953 atoms, 1022 bonds, 45 residues, 1 model selected
> select add #21/D:380
975 atoms, 1046 bonds, 46 residues, 1 model selected
> select add #21/D:381
995 atoms, 1067 bonds, 47 residues, 1 model selected
> select add #21/D:382
1017 atoms, 1091 bonds, 48 residues, 1 model selected
> select add #21/D:383
1037 atoms, 1112 bonds, 49 residues, 1 model selected
> select add #21/D:384
1059 atoms, 1136 bonds, 50 residues, 1 model selected
> select add #21/D:394
1079 atoms, 1157 bonds, 51 residues, 1 model selected
> select add #21/D:395
1101 atoms, 1181 bonds, 52 residues, 1 model selected
> select add #21/D:393
1121 atoms, 1202 bonds, 53 residues, 1 model selected
> select add #21/H:104
1143 atoms, 1226 bonds, 54 residues, 1 model selected
> select subtract #21/H:104
1121 atoms, 1202 bonds, 53 residues, 1 model selected
> select add #21/D:392
1141 atoms, 1223 bonds, 54 residues, 1 model selected
> select add #21/D:391
1163 atoms, 1247 bonds, 55 residues, 1 model selected
> select add #21/D:390
1185 atoms, 1271 bonds, 56 residues, 1 model selected
> select add #21/D:389
1207 atoms, 1295 bonds, 57 residues, 1 model selected
> select add #21/D:388
1229 atoms, 1319 bonds, 58 residues, 1 model selected
> select add #21/D:387
1251 atoms, 1343 bonds, 59 residues, 1 model selected
> select add #21/D:386
1274 atoms, 1368 bonds, 60 residues, 1 model selected
> select add #21/D:385
1296 atoms, 1392 bonds, 61 residues, 1 model selected
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-21.pdb models #21
> selectedOnly true relModel #21
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-21.pdb
Chain information for R-21.pdb #22
---
Chain | Description
D | No description available
> delete atoms sel
> delete bonds sel
> show #!1 models
> select #22/D:411
22 atoms, 24 bonds, 1 residue, 1 model selected
> view matrix models #22,1,0,0,32.601,0,1,0,-6.6747,0,0,1,-4.5262
> view matrix models #22,1,0,0,59.568,0,1,0,-0.43732,0,0,1,58.471
> view matrix models #22,1,0,0,53.335,0,1,0,30.735,0,0,1,28.222
> ui mousemode right "rotate selected models"
> view matrix models
> #22,0.92782,0.04429,-0.3704,150.09,-0.37303,0.1053,-0.92182,479.46,-0.0018247,0.99345,0.11422,75.944
> view matrix models
> #22,0.7605,-0.36885,0.53442,35.908,0.45318,-0.28794,-0.84363,354.44,0.46505,0.88377,-0.051822,37.047
> view matrix models
> #22,0.81848,-0.020995,0.57415,-43.742,0.49794,0.52445,-0.69066,172.81,-0.28661,0.85118,0.4397,80.211
> view matrix models
> #22,0.88778,0.43613,-0.14707,39.222,0.088842,-0.47592,-0.87499,469.32,-0.4516,0.76374,-0.46126,346.05
> view matrix models
> #22,0.8101,0.44431,-0.38253,110.67,-0.068376,-0.57641,-0.8143,504.22,-0.58229,0.68582,-0.43657,380.29
> view matrix models
> #22,0.7929,0.55306,-0.2558,65.594,-0.26409,-0.066437,-0.96221,495.3,-0.54916,0.83049,0.093379,221.74
> ui mousemode right "translate selected models"
> view matrix models
> #22,0.7929,0.55306,-0.2558,65.023,-0.26409,-0.066437,-0.96221,507.62,-0.54916,0.83049,0.093379,204.83
> view matrix models
> #22,0.7929,0.55306,-0.2558,61.573,-0.26409,-0.066437,-0.96221,513.18,-0.54916,0.83049,0.093379,200.72
> ui mousemode right "rotate selected models"
> view matrix models
> #22,0.69503,0.52371,-0.49261,143.81,0.046275,-0.71631,-0.69624,493.26,-0.71749,0.46111,-0.52209,445.53
> view matrix models
> #22,-0.090132,0.54352,-0.83454,385.9,-0.40549,-0.78538,-0.46771,543.67,-0.90964,0.29625,0.29118,317.05
> ui mousemode right "translate selected models"
> view matrix models
> #22,-0.090132,0.54352,-0.83454,376.24,-0.40549,-0.78538,-0.46771,547.05,-0.90964,0.29625,0.29118,311.22
> view matrix models
> #22,-0.090132,0.54352,-0.83454,374.18,-0.40549,-0.78538,-0.46771,545.02,-0.90964,0.29625,0.29118,304.32
> view matrix models
> #22,-0.090132,0.54352,-0.83454,377.5,-0.40549,-0.78538,-0.46771,542.06,-0.90964,0.29625,0.29118,305.61
> view matrix models
> #22,-0.090132,0.54352,-0.83454,376.78,-0.40549,-0.78538,-0.46771,541.81,-0.90964,0.29625,0.29118,306.47
> view matrix models
> #22,-0.090132,0.54352,-0.83454,376.78,-0.40549,-0.78538,-0.46771,541.9,-0.90964,0.29625,0.29118,306.4
> hide #!1 models
> view matrix models
> #22,-0.090132,0.54352,-0.83454,376.37,-0.40549,-0.78538,-0.46771,540.82,-0.90964,0.29625,0.29118,307.28
> view matrix models
> #22,-0.090132,0.54352,-0.83454,375.98,-0.40549,-0.78538,-0.46771,540.43,-0.90964,0.29625,0.29118,307.52
> view matrix models
> #22,-0.090132,0.54352,-0.83454,376.33,-0.40549,-0.78538,-0.46771,540.24,-0.90964,0.29625,0.29118,307.14
> show #!1 models
> hide #!1 models
> select #22/D:416
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #22/D:359
45 atoms, 49 bonds, 2 residues, 1 model selected
> select add #22/D:360
68 atoms, 74 bonds, 3 residues, 1 model selected
> select add #22/D:361
88 atoms, 95 bonds, 4 residues, 1 model selected
> select add #22/D:362
108 atoms, 116 bonds, 5 residues, 1 model selected
> select add #22/D:415
128 atoms, 137 bonds, 6 residues, 1 model selected
> select add #22/D:414
148 atoms, 158 bonds, 7 residues, 1 model selected
> select add #22/D:413
171 atoms, 183 bonds, 8 residues, 1 model selected
> select add #22/D:412
191 atoms, 204 bonds, 9 residues, 1 model selected
> select add #22/D:363
213 atoms, 228 bonds, 10 residues, 1 model selected
> select add #22/D:364
236 atoms, 253 bonds, 11 residues, 1 model selected
> select add #22/D:365
256 atoms, 274 bonds, 12 residues, 1 model selected
> select add #22/D:366
276 atoms, 295 bonds, 13 residues, 1 model selected
> select add #22/D:367
296 atoms, 316 bonds, 14 residues, 1 model selected
> select add #22/D:368
318 atoms, 340 bonds, 15 residues, 1 model selected
> select add #22/D:369
338 atoms, 361 bonds, 16 residues, 1 model selected
> select add #22/D:370
360 atoms, 385 bonds, 17 residues, 1 model selected
> select add #22/D:411
382 atoms, 409 bonds, 18 residues, 1 model selected
> select add #22/D:410
404 atoms, 433 bonds, 19 residues, 1 model selected
> select add #22/D:409
424 atoms, 454 bonds, 20 residues, 1 model selected
> select add #22/D:408
444 atoms, 475 bonds, 21 residues, 1 model selected
> select add #22/D:407
464 atoms, 496 bonds, 22 residues, 1 model selected
> select add #22/D:406
486 atoms, 520 bonds, 23 residues, 1 model selected
> select add #22/D:372
508 atoms, 544 bonds, 24 residues, 1 model selected
> select add #22/D:371
530 atoms, 568 bonds, 25 residues, 1 model selected
> select add #22/D:373
552 atoms, 592 bonds, 26 residues, 1 model selected
> select add #22/D:374
572 atoms, 613 bonds, 27 residues, 1 model selected
> select add #22/D:405
592 atoms, 634 bonds, 28 residues, 1 model selected
> select add #22/D:404
612 atoms, 655 bonds, 29 residues, 1 model selected
> select add #22/D:403
634 atoms, 679 bonds, 30 residues, 1 model selected
> select add #22/D:375
656 atoms, 703 bonds, 31 residues, 1 model selected
> select add #22/D:376
676 atoms, 724 bonds, 32 residues, 1 model selected
> select add #22/D:377
698 atoms, 748 bonds, 33 residues, 1 model selected
> select add #22/D:402
718 atoms, 769 bonds, 34 residues, 1 model selected
> select add #22/D:401
740 atoms, 793 bonds, 35 residues, 1 model selected
> select add #22/D:400
762 atoms, 817 bonds, 36 residues, 1 model selected
> select add #22/D:399
782 atoms, 838 bonds, 37 residues, 1 model selected
> select add #22/D:397
804 atoms, 862 bonds, 38 residues, 1 model selected
> select add #22/D:398
826 atoms, 886 bonds, 39 residues, 1 model selected
> select add #22/D:381
846 atoms, 907 bonds, 40 residues, 1 model selected
> select add #22/D:380
868 atoms, 931 bonds, 41 residues, 1 model selected
> select add #22/D:379
891 atoms, 956 bonds, 42 residues, 1 model selected
> select add #22/D:378
911 atoms, 977 bonds, 43 residues, 1 model selected
> select add #22/D:396
931 atoms, 998 bonds, 44 residues, 1 model selected
> select add #22/D:395
953 atoms, 1022 bonds, 45 residues, 1 model selected
> select add #22/D:394
973 atoms, 1043 bonds, 46 residues, 1 model selected
> select add #22/D:393
993 atoms, 1064 bonds, 47 residues, 1 model selected
> select add #22/D:382
1015 atoms, 1088 bonds, 48 residues, 1 model selected
> select add #22/D:383
1035 atoms, 1109 bonds, 49 residues, 1 model selected
> select add #22/D:384
1057 atoms, 1133 bonds, 50 residues, 1 model selected
> select add #22/D:385
1079 atoms, 1157 bonds, 51 residues, 1 model selected
> select add #22/D:386
1102 atoms, 1182 bonds, 52 residues, 1 model selected
> select add #22/D:387
1124 atoms, 1206 bonds, 53 residues, 1 model selected
> select add #22/D:388
1146 atoms, 1230 bonds, 54 residues, 1 model selected
> select add #22/D:389
1168 atoms, 1254 bonds, 55 residues, 1 model selected
> select add #22/D:390
1190 atoms, 1278 bonds, 56 residues, 1 model selected
> select add #22/D:392
1210 atoms, 1299 bonds, 57 residues, 1 model selected
> select add #22/D:391
1232 atoms, 1323 bonds, 58 residues, 1 model selected
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R21-1.pdb models #22
> selectedOnly true relModel #22
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R21-1.pdb
Chain information for R21-1.pdb #23
---
Chain | Description
D | No description available
> delete atoms sel
> delete bonds sel
> select clear
> select #23/D:402
20 atoms, 21 bonds, 1 residue, 1 model selected
> view matrix models #23,1,0,0,31.661,0,1,0,28.766,0,0,1,-19.39
> view matrix models #23,1,0,0,51.894,0,1,0,53.415,0,0,1,21.675
> ui mousemode right "rotate selected models"
> view matrix models
> #23,0.84862,-0.51482,-0.12168,195.28,0.065385,0.33034,-0.9416,370.51,0.52495,0.7911,0.31399,-52.936
> view matrix models
> #23,0.31409,-0.83914,0.44406,224.57,0.62251,-0.17113,-0.76368,294.15,0.71682,0.5163,0.46862,-84.73
> view matrix models
> #23,0.035268,-0.84629,0.53156,262.92,0.99619,0.072231,0.048903,-14.573,-0.079781,0.52781,0.84561,-10.161
> view matrix models
> #23,0.65019,-0.32329,0.68755,13.902,0.72928,0.51936,-0.44544,85.141,-0.21308,0.79104,0.57345,39.114
> view matrix models
> #23,0.88301,0.46069,0.089827,-20.01,0.043608,0.11003,-0.99297,423.29,-0.46733,0.88072,0.077068,194.81
> view matrix models
> #23,0.2507,0.46378,-0.84974,332.47,-0.29788,-0.79823,-0.52355,529.99,-0.9211,0.38437,-0.061966,401.95
> view matrix models
> #23,-0.016611,0.2627,-0.96474,447.48,-0.31744,-0.91633,-0.24405,487.06,-0.94813,0.30219,0.098612,382.88
> view matrix models
> #23,-0.22401,0.081278,-0.97119,521.24,-0.32747,-0.94486,-0.0035425,436.89,-0.91792,0.31724,0.23827,341.18
> ui mousemode right "translate selected models"
> view matrix models
> #23,-0.22401,0.081278,-0.97119,507.69,-0.32747,-0.94486,-0.0035425,436.52,-0.91792,0.31724,0.23827,332.72
> view matrix models
> #23,-0.22401,0.081278,-0.97119,507.04,-0.32747,-0.94486,-0.0035425,436.9,-0.91792,0.31724,0.23827,332.39
> view matrix models
> #23,-0.22401,0.081278,-0.97119,507.5,-0.32747,-0.94486,-0.0035425,429.18,-0.91792,0.31724,0.23827,335.76
> view matrix models
> #23,-0.22401,0.081278,-0.97119,506.69,-0.32747,-0.94486,-0.0035425,427.4,-0.91792,0.31724,0.23827,335.91
> view matrix models
> #23,-0.22401,0.081278,-0.97119,507.21,-0.32747,-0.94486,-0.0035425,427.46,-0.91792,0.31724,0.23827,336.02
> view matrix models
> #23,-0.22401,0.081278,-0.97119,507.57,-0.32747,-0.94486,-0.0035425,429.03,-0.91792,0.31724,0.23827,334.92
> show #!1 models
> view matrix models
> #23,-0.22401,0.081278,-0.97119,508.96,-0.32747,-0.94486,-0.0035425,438.13,-0.91792,0.31724,0.23827,327.9
> ui mousemode right "rotate selected models"
> view matrix models
> #23,-0.029609,0.39528,-0.91808,405.29,-0.1057,-0.91457,-0.39036,478.63,-0.99396,0.085487,0.068863,421.03
> view matrix models
> #23,-0.43495,0.11721,-0.89279,528.17,-0.28227,-0.95926,0.011587,427.51,-0.85507,0.25705,0.45032,274.43
> view matrix models
> #23,-0.094745,0.39418,-0.91413,417.95,-0.23357,-0.90144,-0.3645,496.95,-0.96771,0.17898,0.17747,374.84
> view matrix models
> #23,0.060323,0.47489,-0.87797,364.22,-0.26458,-0.84051,-0.4728,519.11,-0.96248,0.26081,0.074944,384.73
> view matrix models
> #23,-0.16469,0.37084,-0.91398,436.16,-0.32472,-0.89536,-0.30478,500.77,-0.93136,0.24659,0.26787,335.03
> ui mousemode right "translate selected models"
> view matrix models
> #23,-0.16469,0.37084,-0.91398,441.84,-0.32472,-0.89536,-0.30478,498.28,-0.93136,0.24659,0.26787,335.65
> view matrix models
> #23,-0.16469,0.37084,-0.91398,443.22,-0.32472,-0.89536,-0.30478,497.64,-0.93136,0.24659,0.26787,334.82
> view matrix models
> #23,-0.16469,0.37084,-0.91398,438.99,-0.32472,-0.89536,-0.30478,496.57,-0.93136,0.24659,0.26787,333.24
> view matrix models
> #23,-0.16469,0.37084,-0.91398,441.78,-0.32472,-0.89536,-0.30478,495.31,-0.93136,0.24659,0.26787,331.91
> view matrix models
> #23,-0.16469,0.37084,-0.91398,439.87,-0.32472,-0.89536,-0.30478,494.87,-0.93136,0.24659,0.26787,331.91
> view matrix models
> #23,-0.16469,0.37084,-0.91398,442.27,-0.32472,-0.89536,-0.30478,492.32,-0.93136,0.24659,0.26787,329.29
> view matrix models
> #23,-0.16469,0.37084,-0.91398,437.59,-0.32472,-0.89536,-0.30478,492.19,-0.93136,0.24659,0.26787,331.85
> view matrix models
> #23,-0.16469,0.37084,-0.91398,437.6,-0.32472,-0.89536,-0.30478,492.16,-0.93136,0.24659,0.26787,331.89
> volume #1 level 3.29
> volume #1 level 4.85
> volume #1 level 3.178
> volume #1 level 2.844
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-21.pdb
Chain information for R-21.pdb #24
---
Chain | Description
D | No description available
> close #24
> combine #20 #18
Remapping chain ID 'B' in fold_r_e_m_model_3.cif #18 to 'D'
> hide #!21 models
> hide #22 models
> hide #23 models
> select #24/H:541
23 atoms, 25 bonds, 1 residue, 1 model selected
> view matrix models #24,1,0,0,-19.338,0,1,0,-30.373,0,0,1,54.63
> view matrix models #24,1,0,0,-9.2457,0,1,0,26.006,0,0,1,20.565
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.20314,0.82199,0.53204,-22.855,-0.050577,0.53384,-0.84407,303.25,-0.97784,-0.19838,-0.066871,490.21
> view matrix models
> #24,-0.84714,0.3771,-0.37436,387.68,0.465,0.18518,-0.86573,264,-0.25714,-0.90747,-0.33223,526.39
> view matrix models
> #24,-0.59609,0.74776,-0.29247,250.29,-0.26791,-0.52862,-0.80547,533.36,-0.7569,-0.40177,0.51544,355.8
> view matrix models
> #24,-0.60438,0.78241,-0.15021,215.05,-0.24119,-0.35938,-0.90148,517.68,-0.75931,-0.50861,0.40591,399.35
> view matrix models
> #24,-0.62855,0.75276,-0.19565,235.27,-0.20322,-0.40176,-0.89291,515.64,-0.75076,-0.52148,0.4055,400
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.62855,0.75276,-0.19565,243.83,-0.20322,-0.40176,-0.89291,508.04,-0.75076,-0.52148,0.4055,420.59
> view matrix models
> #24,-0.62855,0.75276,-0.19565,246.06,-0.20322,-0.40176,-0.89291,512.51,-0.75076,-0.52148,0.4055,412.99
> fitmap #24 inMap #1
Fit molecule combination (#24) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 12183 atoms
average map value = 3.543, steps = 240
shifted from previous position = 11.2
rotated from previous position = 26.8 degrees
atoms outside contour = 4369, contour level = 2.8438
Position of combination (#24) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.47578467 0.87186953 0.11607097 131.08230032
-0.61316610 -0.23416980 -0.75444804 541.87541903
-0.63059995 -0.43012559 0.64601524 313.11404992
Axis 0.19150712 0.44089699 -0.87688931
Axis point 271.97831464 307.70470298 0.00000000
Rotation angle (degrees) 122.13863044
Shift along axis -10.55192821
> hide #!24 models
> show #!20 models
> hide #!20 models
> show #!21 models
> show #22 models
> show #23 models
> volume #1 level 1.417
> volume #1 level 0.9492
> select #23/D:397
22 atoms, 24 bonds, 1 residue, 1 model selected
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> view matrix models
> #23,0.064294,0.22331,-0.97262,427.84,0.51162,-0.84418,-0.16,275.98,-0.8568,-0.48733,-0.16853,538.23
> view matrix models
> #23,-0.32366,-0.41661,-0.84951,583.02,0.53281,-0.82221,0.20022,182.78,-0.78189,-0.38782,0.48809,351.27
> view matrix models
> #23,-0.2721,-0.84305,-0.46393,550.23,0.67106,-0.51178,0.53643,24.494,-0.68967,-0.16536,0.70499,245.14
> ui mousemode right "translate selected models"
> view matrix models
> #23,-0.2721,-0.84305,-0.46393,561.47,0.67106,-0.51178,0.53643,25.485,-0.68967,-0.16536,0.70499,240.68
> view matrix models
> #23,-0.2721,-0.84305,-0.46393,563.68,0.67106,-0.51178,0.53643,25.225,-0.68967,-0.16536,0.70499,240.91
> view matrix models
> #23,-0.2721,-0.84305,-0.46393,552.81,0.67106,-0.51178,0.53643,39.033,-0.68967,-0.16536,0.70499,245.5
> view matrix models
> #23,-0.2721,-0.84305,-0.46393,563.06,0.67106,-0.51178,0.53643,44.25,-0.68967,-0.16536,0.70499,248.62
> view matrix models
> #23,-0.2721,-0.84305,-0.46393,564.22,0.67106,-0.51178,0.53643,42.845,-0.68967,-0.16536,0.70499,250.93
> ui mousemode right "rotate selected models"
> view matrix models
> #23,-0.24549,-0.94209,-0.22847,519.08,0.7231,-0.33493,0.60412,-12.458,-0.64565,-0.016898,0.76344,204.09
> view matrix models
> #23,-0.13133,-0.97875,-0.15749,484.54,0.98867,-0.14097,0.051618,31.887,-0.072722,-0.14893,0.98617,53.847
> view matrix models
> #23,-0.28724,-0.89745,-0.33478,545.72,0.90219,-0.3709,0.22019,46.994,-0.32178,-0.23879,0.91621,136.56
> view matrix models
> #23,-0.15331,-0.94952,-0.27369,511.88,0.97498,-0.10022,-0.19843,87.247,0.16099,-0.29727,0.94112,39.928
> view matrix models
> #23,-0.44419,-0.75747,-0.47848,589.63,0.81328,-0.56494,0.13933,115.89,-0.37585,-0.32725,0.86698,173.6
> view matrix models
> #23,-0.23981,-0.96402,-0.11468,494.54,0.95582,-0.25513,0.14597,34.87,-0.16998,-0.074607,0.98262,62.855
> view matrix models
> #23,-0.0071859,-0.98983,-0.14207,456.87,0.80742,0.078073,-0.58478,184.74,0.58993,-0.11891,0.79865,-44.325
> view matrix models
> #23,-0.23882,-0.95304,-0.18625,509.48,0.41675,0.072648,-0.90611,342.7,0.87709,-0.29402,0.37983,23.28
> view matrix models
> #23,-0.34726,-0.93451,-0.078079,503.44,0.90886,-0.3559,0.21748,43.973,-0.23102,0.0045591,0.97294,64.946
> view matrix models
> #23,0.091613,-0.93753,0.33562,314.94,0.99577,0.088746,-0.023906,11.287,-0.0073722,0.33639,0.9417,-27.665
> view matrix models
> #23,0.41497,-0.78543,0.45923,193.99,0.8975,0.27054,-0.3483,78.786,0.14932,0.55669,0.81719,-66.573
> view matrix models
> #23,0.69213,-0.64708,0.31976,147.08,0.45783,0.051106,-0.88757,332.68,0.55799,0.76071,0.33163,-69.756
> view matrix models
> #23,0.74826,-0.65147,0.12528,182.17,-0.070195,-0.26553,-0.96154,510.67,0.65968,0.71069,-0.24442,53.518
> view matrix models
> #23,0.78354,-0.62064,0.029525,192.52,-0.16082,-0.24848,-0.95519,525.17,0.60016,0.74369,-0.29451,72.354
> view matrix models
> #23,0.54918,-0.64975,0.52557,128.6,0.057002,-0.59831,-0.79924,499.74,0.83376,0.46889,-0.29154,67.773
> view matrix models
> #23,0.43169,-0.4834,0.76156,70.304,0.86117,-0.030324,-0.5074,172.39,0.26837,0.87487,0.4032,-44.75
> view matrix models
> #23,0.54907,-0.4106,0.72796,42.134,0.77923,-0.063452,-0.62352,222.14,0.30221,0.9096,0.28511,-29.508
> view matrix models
> #23,0.74024,-0.26901,0.61617,6.0575,0.61721,-0.091537,-0.78145,297.57,0.26662,0.95878,0.098278,14.065
> view matrix models
> #23,0.94717,-0.088736,0.3082,6.9411,0.27877,-0.24733,-0.92796,427.54,0.15857,0.96486,-0.20953,108.3
> view matrix models
> #23,0.99778,0.021082,0.063133,36.65,0.066551,-0.33131,-0.94117,488.33,0.0010749,0.94329,-0.33198,173.5
> view matrix models
> #23,0.89801,-0.10747,0.42666,-7.7937,0.29801,-0.56484,-0.76951,437.46,0.32369,0.81817,-0.4752,160.55
> view matrix models
> #23,0.63192,-0.15736,0.75889,-23.261,0.54561,-0.6051,-0.57979,347.67,0.55044,0.78044,-0.29652,77.291
> view matrix models
> #23,0.70143,-0.10438,0.70506,-33.477,0.59235,-0.46477,-0.65811,333.87,0.39638,0.87926,-0.26417,85.611
> view matrix models
> #23,0.91517,-0.031873,0.4018,-17.706,0.31604,-0.56195,-0.76442,432.07,0.25016,0.82656,-0.50421,181.31
> view matrix models
> #23,0.99522,-0.089741,-0.038602,79.086,-0.092516,-0.73889,-0.66744,522.59,0.031374,0.66782,-0.74366,309.1
> view matrix models
> #23,0.92602,-0.033088,0.37602,-13.663,0.017253,-0.9914,-0.12973,413.43,0.37708,0.12662,-0.91748,365.73
> view matrix models
> #23,0.97969,0.1284,0.15401,1.5461,0.19941,-0.70443,-0.68119,459.74,0.021027,0.69806,-0.71573,299.36
> view matrix models
> #23,0.9832,0.14284,0.11363,8.0126,0.17943,-0.64221,-0.74523,468.93,-0.033479,0.7531,-0.65705,287.9
> view matrix models
> #23,0.97987,0.070186,-0.18692,91.397,-0.046034,-0.83153,-0.55357,501.18,-0.19428,0.55102,-0.81156,390.5
> view matrix models
> #23,0.85566,0.18013,0.48518,-59.401,0.44622,-0.73168,-0.5153,373.72,0.26217,0.65742,-0.70644,253.62
> view matrix models
> #23,0.87513,0.18714,0.44623,-55.356,0.43844,-0.69685,-0.5676,382.08,0.20473,0.69237,-0.69189,256.43
> ui mousemode right "translate selected models"
> view matrix models
> #23,0.87513,0.18714,0.44623,-52.579,0.43844,-0.69685,-0.5676,377.89,0.20473,0.69237,-0.69189,260.07
> view matrix models
> #23,0.87513,0.18714,0.44623,-59.092,0.43844,-0.69685,-0.5676,381.85,0.20473,0.69237,-0.69189,263.99
> view matrix models
> #23,0.87513,0.18714,0.44623,-59.622,0.43844,-0.69685,-0.5676,383.28,0.20473,0.69237,-0.69189,266.35
> view matrix models
> #23,0.87513,0.18714,0.44623,-48.224,0.43844,-0.69685,-0.5676,385.76,0.20473,0.69237,-0.69189,263.73
> view matrix models
> #23,0.87513,0.18714,0.44623,-51.107,0.43844,-0.69685,-0.5676,388.21,0.20473,0.69237,-0.69189,264.26
> view matrix models
> #23,0.87513,0.18714,0.44623,-52.087,0.43844,-0.69685,-0.5676,389.62,0.20473,0.69237,-0.69189,266.74
> ui mousemode right "rotate selected models"
> view matrix models
> #23,0.95986,0.044769,0.27687,-6.5442,0.27371,-0.3649,-0.88991,446.32,0.06119,0.92997,-0.36251,180.12
> ui mousemode right "translate selected models"
> view matrix models
> #23,0.95986,0.044769,0.27687,-2.0721,0.27371,-0.3649,-0.88991,434.52,0.06119,0.92997,-0.36251,172.74
> view matrix models
> #23,0.95986,0.044769,0.27687,2.3532,0.27371,-0.3649,-0.88991,431.35,0.06119,0.92997,-0.36251,172.47
> view matrix models
> #23,0.95986,0.044769,0.27687,1.4998,0.27371,-0.3649,-0.88991,432.41,0.06119,0.92997,-0.36251,170.05
> view matrix models
> #23,0.95986,0.044769,0.27687,3.1717,0.27371,-0.3649,-0.88991,433.48,0.06119,0.92997,-0.36251,167.63
> view matrix models
> #23,0.95986,0.044769,0.27687,3.3564,0.27371,-0.3649,-0.88991,434.7,0.06119,0.92997,-0.36251,166.83
> view matrix models
> #23,0.95986,0.044769,0.27687,1.7153,0.27371,-0.3649,-0.88991,433.52,0.06119,0.92997,-0.36251,167.82
> view matrix models
> #23,0.95986,0.044769,0.27687,2.2868,0.27371,-0.3649,-0.88991,432.23,0.06119,0.92997,-0.36251,167.68
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #21/D:358
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #21/D:357
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add #21/D:356
62 atoms, 66 bonds, 3 residues, 1 model selected
> select add #21/D:424
84 atoms, 90 bonds, 4 residues, 1 model selected
> select add #21/D:423
104 atoms, 111 bonds, 5 residues, 1 model selected
> select add #21/D:422
124 atoms, 132 bonds, 6 residues, 1 model selected
> select add #21/D:421
144 atoms, 153 bonds, 7 residues, 1 model selected
> select add #21/D:420
167 atoms, 178 bonds, 8 residues, 1 model selected
> select add #21/C:419
187 atoms, 199 bonds, 9 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> open
> /Users/lingxiaobin/Desktop/ROOL:GOLLD/fold_2024_07_21_21_09/fold_2024_07_21_21_09_model_0.cif
Chain information for fold_2024_07_21_21_09_model_0.cif #25
---
Chain | Description
A | .
> open
> /Users/lingxiaobin/Desktop/ROOL:GOLLD/fold_2024_07_21_21_09/fold_2024_07_21_21_09_model_1.cif
Chain information for fold_2024_07_21_21_09_model_1.cif #26
---
Chain | Description
A | .
> open
> /Users/lingxiaobin/Desktop/ROOL:GOLLD/fold_2024_07_21_21_09/fold_2024_07_21_21_09_model_2.cif
Chain information for fold_2024_07_21_21_09_model_2.cif #27
---
Chain | Description
A | .
> open
> /Users/lingxiaobin/Desktop/ROOL:GOLLD/fold_2024_07_21_21_09/fold_2024_07_21_21_09_model_4.cif
Chain information for fold_2024_07_21_21_09_model_4.cif #28
---
Chain | Description
A | .
> open
> /Users/lingxiaobin/Desktop/ROOL:GOLLD/fold_2024_07_21_21_09/fold_2024_07_21_21_09_model_3.cif
Chain information for fold_2024_07_21_21_09_model_3.cif #29
---
Chain | Description
A | .
> hide #26 models
> hide #27 models
> hide #28 models
> hide #29 models
> select clear
> select #25/A:1@P
1 atom, 1 residue, 1 model selected
> select clear
> select #25/A:9@O3'
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
212 atoms, 236 bonds, 10 residues, 1 model selected
> cartoon sel
> view matrix models #25,1,0,0,64.557,0,1,0,-64.617,0,0,1,161.57
> view matrix models #25,1,0,0,173.71,0,1,0,35.303,0,0,1,326.95
> view matrix models #25,1,0,0,208.82,0,1,0,208.9,0,0,1,226.84
> view matrix models #25,1,0,0,213.09,0,1,0,222.37,0,0,1,231.01
> view matrix models #25,1,0,0,203.01,0,1,0,223.96,0,0,1,263.21
> ui mousemode right "rotate selected models"
> view matrix models
> #25,-0.27395,0.93532,0.22387,204.65,-0.91631,-0.32454,0.23461,223.99,0.29209,-0.14087,0.94596,262.9
> view matrix models
> #25,-0.26501,-0.17714,0.94784,204.37,0.63373,-0.77286,0.032749,222.5,0.72675,0.60935,0.31707,262.68
> view matrix models
> #25,-0.26097,0.83896,0.47753,204.66,0.92795,0.081654,0.36366,222.91,0.2661,0.53803,-0.79982,262.4
> view matrix models
> #25,-0.64683,0.60528,0.46395,204.79,0.68261,0.1882,0.70613,223.3,0.34009,0.77345,-0.5349,262.6
> view matrix models
> #25,-0.69278,0.31541,0.64852,204.73,0.65466,-0.1021,0.749,223.15,0.30245,0.94345,-0.13575,262.92
> ui mousemode right "translate selected models"
> view matrix models
> #25,-0.69278,0.31541,0.64852,188.08,0.65466,-0.1021,0.749,243.74,0.30245,0.94345,-0.13575,260.43
> view matrix models
> #25,-0.69278,0.31541,0.64852,187.38,0.65466,-0.1021,0.749,246.23,0.30245,0.94345,-0.13575,257.9
> show #!1 models
> view matrix models
> #25,-0.69278,0.31541,0.64852,190.37,0.65466,-0.1021,0.749,250.16,0.30245,0.94345,-0.13575,262.36
> view matrix models
> #25,-0.69278,0.31541,0.64852,191.51,0.65466,-0.1021,0.749,247.4,0.30245,0.94345,-0.13575,260.36
> view matrix models
> #25,-0.69278,0.31541,0.64852,192.24,0.65466,-0.1021,0.749,247.09,0.30245,0.94345,-0.13575,260.11
> view matrix models
> #25,-0.69278,0.31541,0.64852,193.2,0.65466,-0.1021,0.749,249.62,0.30245,0.94345,-0.13575,261.55
> ui mousemode right "rotate selected models"
> view matrix models
> #25,-0.79171,0.077526,0.60596,193.09,0.59628,-0.11762,0.79411,249.67,0.13283,0.99003,0.04689,261.8
> view matrix models
> #25,-0.78864,-0.19178,0.58418,192.88,0.6111,-0.13962,0.77914,249.66,-0.067854,0.97146,0.22731,262.04
> view matrix models
> #25,-0.76102,0.10571,0.64006,193.08,0.6225,-0.1587,0.76636,249.63,0.18258,0.98165,0.054969,261.76
> view matrix models
> #25,-0.78212,0.08148,0.61778,193.07,0.60126,-0.16171,0.78252,249.66,0.16366,0.98347,0.077484,261.79
> hide #!21 models
> hide #22 models
> hide #23 models
> hide #25 models
> show #25 models
> fitmap #25 inMap #1
Fit molecule fold_2024_07_21_21_09_model_0.cif (#25) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 212 atoms
average map value = 4.666, steps = 376
shifted from previous position = 2.92
rotated from previous position = 43.1 degrees
atoms outside contour = 10, contour level = 0.94917
Position of fold_2024_07_21_21_09_model_0.cif (#25) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.97931188 0.18595263 -0.07981134 190.97410893
-0.07992567 0.00689399 0.99677698 248.57100386
0.18590352 0.98253452 0.00811102 261.73519212
Axis -0.03786249 -0.70638249 -0.70681696
Axis point 87.72181431 -18.38563361 0.00000000
Rotation angle (degrees) 169.15915977
Shift along axis -367.81583137
> show #26 models
> hide #25 models
> hide #!1 models
> show #27 models
> hide #26 models
> select add #26
424 atoms, 472 bonds, 20 residues, 2 models selected
> select subtract #26
212 atoms, 236 bonds, 10 residues, 1 model selected
> hide #27 models
> show #28 models
> show #29 models
> hide #28 models
> show #25 models
> hide #29 models
> close #26-29
> show #!1 models
> open
> /Users/lingxiaobin/Desktop/ROOL:GOLLD/fold_2024_07_21_21_10/fold_2024_07_21_21_10_model_0.cif
Chain information for fold_2024_07_21_21_10_model_0.cif #26
---
Chain | Description
A | .
> show #!21 models
> show #22 models
> show #23 models
> select clear
> select #26/A:5
20 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #26,1,0,0,-37.406,0,1,0,-37.558,0,0,1,166.04
> view matrix models #26,1,0,0,159.04,0,1,0,158.57,0,0,1,370.15
> view matrix models #26,1,0,0,229.41,0,1,0,232.87,0,0,1,333.76
> view matrix models #26,1,0,0,209.95,0,1,0,253.76,0,0,1,260.35
> view matrix models #26,1,0,0,156.66,0,1,0,242.37,0,0,1,248.09
> view matrix models #26,1,0,0,173.19,0,1,0,234.27,0,0,1,275.46
> hide #!1 models
> ui mousemode right "translate selected models"
> view matrix models #26,1,0,0,183.85,0,1,0,203.59,0,0,1,282.37
> select clear
> select #25/A:2
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #25/A:1
23 atoms, 25 bonds, 1 residue, 1 model selected
> show #!1 models
> ui mousemode right "translate selected atoms"
> hide #!1 models
> select #26/A:5
20 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #26,-0.11652,0.935,0.33496,190.83,-0.99158,-0.12873,0.014379,210,0.056562,-0.33046,0.94212,281.94
> view matrix models
> #26,-0.31075,0.31654,0.89624,193.52,-0.78516,-0.61691,-0.054352,208.87,0.53569,-0.72057,0.44023,278.21
> view matrix models
> #26,0.57188,0.47292,0.6703,188.23,-0.62064,-0.28489,0.73051,210.12,0.53643,-0.83378,0.13059,277.33
> view matrix models
> #26,0.84584,0.50725,0.16507,185.62,-0.20766,0.028069,0.9778,208.23,0.49136,-0.86134,0.12908,277.59
> view matrix models
> #26,0.30803,0.75296,0.58153,189.5,-0.53412,-0.36896,0.76065,209.67,0.7873,-0.54491,0.28851,276.17
> view matrix models
> #26,-0.12492,-0.73172,-0.67006,188.84,0.67588,-0.55717,0.48244,202.44,-0.72635,-0.39261,0.56416,285.02
> view matrix models
> #26,-0.17632,-0.96465,-0.19585,189.9,0.71347,-0.26232,0.64973,202.64,-0.67814,-0.025171,0.7345,285.19
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.17632,-0.96465,-0.19585,190.5,0.71347,-0.26232,0.64973,216.45,-0.67814,-0.025171,0.7345,275.07
> show #!1 models
> ui mousemode right "rotate selected models"
> view matrix models
> #26,-0.39399,-0.46744,-0.79137,190.57,0.39214,-0.86421,0.31523,217.68,-0.83126,-0.18613,0.5238,275.41
> view matrix models
> #26,-0.84595,-0.51947,0.12054,194.74,0.46799,-0.61482,0.63481,217.73,-0.25565,0.59342,0.76321,272.58
> view matrix models
> #26,-0.99321,0.10117,0.057374,195.41,-0.020166,-0.63565,0.77172,220.84,0.11454,0.76532,0.63337,270.16
> view matrix models
> #26,-0.73326,-0.16056,0.66072,195.55,0.61753,-0.56395,0.54828,217.07,0.28458,0.81005,0.51268,269.01
> view matrix models
> #26,-0.64925,-0.043176,0.75935,195.3,0.35278,-0.90159,0.25037,217.86,0.67381,0.43043,0.60059,267.1
> view matrix models
> #26,-0.8268,0.44906,0.33875,195.3,-0.19655,-0.7949,0.57402,221.18,0.52704,0.40802,0.74548,268.1
> view matrix models
> #26,-0.88067,0.47334,0.019463,194.84,-0.39064,-0.74882,0.53541,222.06,0.268,0.46391,0.84437,269.61
> view matrix models
> #26,-0.96238,0.27171,0.0029237,195.16,-0.23479,-0.83695,0.49436,221.12,0.13677,0.47507,0.86925,270.36
> view matrix models
> #26,-0.86966,-0.48339,-0.1001,194.17,0.41953,-0.8306,0.36619,217.05,-0.26015,0.27647,0.92514,272.75
> view matrix models
> #26,-0.94633,-0.318,0.057773,195.07,0.29752,-0.78724,0.54013,218.04,-0.12628,0.52833,0.8396,271.77
> view matrix models
> #26,-0.81961,-0.54061,0.1897,194.64,0.55483,-0.66639,0.49809,216.47,-0.14286,0.51349,0.84612,271.88
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.81961,-0.54061,0.1897,191.94,0.55483,-0.66639,0.49809,223.15,-0.14286,0.51349,0.84612,269.81
> view matrix models
> #26,-0.81961,-0.54061,0.1897,192.21,0.55483,-0.66639,0.49809,222.47,-0.14286,0.51349,0.84612,269.27
> view matrix models
> #26,-0.81961,-0.54061,0.1897,193.99,0.55483,-0.66639,0.49809,223.84,-0.14286,0.51349,0.84612,265.89
> ui mousemode right "rotate selected models"
> view matrix models
> #26,-0.76479,-0.14731,0.62721,194.87,0.62368,-0.41347,0.66337,223.94,0.16161,0.89852,0.4081,263.4
> view matrix models
> #26,-0.48971,-0.67165,0.55595,193.06,0.85148,-0.23128,0.47062,222.46,-0.18752,0.70385,0.68515,265.68
> view matrix models
> #26,-0.48121,-0.66664,0.56924,193.04,0.85729,-0.22232,0.46436,222.41,-0.18301,0.71146,0.67848,265.64
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.48121,-0.66664,0.56924,195.4,0.85729,-0.22232,0.46436,227.71,-0.18301,0.71146,0.67848,269.94
> hide #!1 models
> volume #1 level 1.506
> volume #1 level 3.557
> select #1
3 models selected
> select clear
> ui mousemode right "rotate selected models"
> view matrix models
> #25,-0.97676,-0.13681,0.16498,191.44,0.15603,0.073839,0.98499,248.35,-0.14694,0.98784,-0.050776,261.9
> view matrix models
> #25,-0.9034,-0.18653,-0.3861,190.2,-0.33668,-0.24904,0.90809,248.71,-0.26555,0.95036,0.16218,262.35
> view matrix models
> #25,-0.99773,0.066771,-0.008197,191.01,-0.036445,-0.43408,0.90014,248.45,0.056545,0.8984,0.43553,262.5
> view matrix models
> #25,-0.95972,-0.12829,0.24997,191.34,0.27945,-0.5281,0.80189,247.95,0.029132,0.83944,0.54268,262.68
> view matrix models
> #25,-0.52345,0.3031,0.79632,191.93,0.65306,-0.45756,0.60344,247.26,0.54727,0.83592,0.041571,261.28
> view matrix models
> #25,-0.79373,0.56554,0.22395,191.16,0.34322,0.11244,0.9325,248.14,0.50218,0.81702,-0.28336,260.75
> view matrix models
> #25,-0.85376,0.40252,0.33026,191.42,0.37326,0.030943,0.92721,248.11,0.363,0.91489,-0.17666,261.05
> view matrix models
> #25,-0.81858,0.0031126,0.57439,191.82,0.56315,-0.19259,0.8036,247.74,0.11312,0.98128,0.15589,261.84
> ui mousemode right "translate selected models"
> view matrix models
> #25,-0.81858,0.0031126,0.57439,192.52,0.56315,-0.19259,0.8036,251.26,0.11312,0.98128,0.15589,258.77
> view matrix models
> #25,-0.81858,0.0031126,0.57439,193.99,0.56315,-0.19259,0.8036,251.53,0.11312,0.98128,0.15589,261.4
> ui mousemode right "rotate selected models"
> view matrix models
> #25,-0.77913,-0.50655,0.36927,193.5,0.52316,-0.2009,0.82822,251.64,-0.34535,0.83848,0.42154,262.23
> view matrix models
> #25,-0.97685,-0.041036,0.20996,193.59,0.19372,-0.58608,0.78675,251.76,0.090766,0.80921,0.58046,262.06
> view matrix models
> #25,-0.96562,0.053265,0.25445,193.7,0.16814,-0.61852,0.76757,251.73,0.19827,0.78396,0.5883,261.97
> ui mousemode right "translate selected models"
> view matrix models
> #25,-0.96562,0.053265,0.25445,192.56,0.16814,-0.61852,0.76757,251.61,0.19827,0.78396,0.5883,259.88
> view matrix models
> #25,-0.96562,0.053265,0.25445,192.83,0.16814,-0.61852,0.76757,250.44,0.19827,0.78396,0.5883,259.05
> view matrix models
> #25,-0.96562,0.053265,0.25445,193.04,0.16814,-0.61852,0.76757,251.37,0.19827,0.78396,0.5883,259.49
> view matrix models
> #25,-0.96562,0.053265,0.25445,193.69,0.16814,-0.61852,0.76757,251.62,0.19827,0.78396,0.5883,257.76
> view matrix models
> #25,-0.96562,0.053265,0.25445,193.94,0.16814,-0.61852,0.76757,250.58,0.19827,0.78396,0.5883,258.25
> view matrix models
> #25,-0.96562,0.053265,0.25445,194.69,0.16814,-0.61852,0.76757,252.47,0.19827,0.78396,0.5883,258.82
> fitmap #25 inMap #1
Fit molecule fold_2024_07_21_21_09_model_0.cif (#25) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 212 atoms
average map value = 4.576, steps = 104
shifted from previous position = 7.55
rotated from previous position = 43.3 degrees
atoms outside contour = 45, contour level = 3.557
Position of fold_2024_07_21_21_09_model_0.cif (#25) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.98432059 0.13602780 -0.11229159 191.16442984
-0.10998039 0.02441243 0.99363390 248.46172903
0.13790315 0.99040419 -0.00906927 262.57396809
Axis -0.00920420 -0.71301718 -0.70108615
Axis point 93.47780006 0.00000000 20.77934306
Rotation angle (degrees) 169.89527540
Shift along axis -363.00396800
> select #26/A:10
22 atoms, 24 bonds, 1 residue, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #26,0.25803,0.53856,0.80211,191.36,0.60262,0.55921,-0.56933,226.49,-0.75516,0.63027,-0.18025,270.83
> view matrix models
> #26,-0.33711,0.26732,0.90271,194.95,0.32707,0.93237,-0.15396,229.12,-0.88282,0.24335,-0.40175,270.92
> view matrix models
> #26,0.49335,0.59994,0.62982,189.79,0.44292,0.4499,-0.77551,226.83,-0.74861,0.66156,-0.04377,271.16
> ui mousemode right "translate selected models"
> view matrix models
> #26,0.49335,0.59994,0.62982,188.47,0.44292,0.4499,-0.77551,218.01,-0.74861,0.66156,-0.04377,303.78
> view matrix models
> #26,0.49335,0.59994,0.62982,188.44,0.44292,0.4499,-0.77551,220.09,-0.74861,0.66156,-0.04377,303.7
> ui mousemode right "rotate selected models"
> view matrix models
> #26,0.47287,0.5999,0.64538,188.58,0.76656,0.081105,-0.63704,218.64,-0.4345,0.79596,-0.4215,301.35
> view matrix models
> #26,0.48303,0.59864,0.639,188.51,0.63651,0.26108,-0.72574,219.18,-0.60129,0.75727,-0.25493,302.49
> ui mousemode right "translate selected models"
> view matrix models
> #26,0.48303,0.59864,0.639,189.06,0.63651,0.26108,-0.72574,222.71,-0.60129,0.75727,-0.25493,307.2
> view matrix models
> #26,0.48303,0.59864,0.639,189.71,0.63651,0.26108,-0.72574,222.74,-0.60129,0.75727,-0.25493,303.03
> fitmap #26 inMap #1
Fit molecule fold_2024_07_21_21_10_model_0.cif (#26) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 427 atoms
average map value = 4.518, steps = 84
shifted from previous position = 4.9
rotated from previous position = 8.37 degrees
atoms outside contour = 105, contour level = 3.557
Position of fold_2024_07_21_21_10_model_0.cif (#26) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.37058142 0.67734900 0.63550588 193.69845121
0.62409918 0.32514254 -0.71048050 223.50404389
-0.68787326 0.65990957 -0.30224117 306.41714073
Axis 0.71905664 0.69438956 -0.02794069
Axis point 0.00000000 -141.62680560 169.66518304
Rotation angle (degrees) 107.65342815
Shift along axis 285.91752733
> hide #!1 models
> show #!1 models
> hide #25 models
> show #25 models
> hide #26 models
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/R_249-277.pdb
Chain information for R_249-277.pdb #27
---
Chain | Description
A | No description available
> select #27/A:263
23 atoms, 25 bonds, 1 residue, 1 model selected
> view matrix models #27,1,0,0,33.626,0,1,0,-40.8,0,0,1,166.07
> view matrix models #27,1,0,0,33.952,0,1,0,-41.19,0,0,1,167.96
> ui mousemode right "rotate selected models"
> view matrix models
> #27,0.99994,-0.010064,0.0050354,35.923,0.010045,0.99994,0.0037776,-43.26,-0.0050732,-0.0037268,0.99998,169.74
> view matrix models
> #27,0.45904,-0.80262,0.38089,277.17,0.4917,0.5866,0.64353,-97.842,-0.73994,-0.10812,0.66393,358.27
> view matrix models
> #27,-0.28866,-0.75727,0.58585,352.41,0.030826,0.60423,0.79621,-52.396,-0.95693,0.2479,-0.15107,411.67
> view matrix models
> #27,-0.11036,-0.74334,0.65975,310.68,0.16723,0.64045,0.74957,-76.621,-0.97972,0.19305,0.053628,401.09
> view matrix models
> #27,-0.50779,-0.71375,-0.48241,524.23,-0.51136,-0.20093,0.83555,239.38,-0.6933,0.67097,-0.26295,274.41
> view matrix models
> #27,-0.34833,-0.49932,-0.79332,486.11,-0.72387,-0.39442,0.56608,361.2,-0.59555,0.77144,-0.22405,227.23
> view matrix models
> #27,-0.33386,-0.51262,-0.79105,487.07,-0.74233,-0.37422,0.5558,360.15,-0.58094,0.77278,-0.25559,229.02
> ui mousemode right "translate selected models"
> view matrix models
> #27,-0.33386,-0.51262,-0.79105,486.25,-0.74233,-0.37422,0.5558,360.05,-0.58094,0.77278,-0.25559,222.96
> view matrix models
> #27,-0.33386,-0.51262,-0.79105,494.09,-0.74233,-0.37422,0.5558,360.65,-0.58094,0.77278,-0.25559,226.82
> view matrix models
> #27,-0.33386,-0.51262,-0.79105,494.11,-0.74233,-0.37422,0.5558,360.96,-0.58094,0.77278,-0.25559,222.08
> view matrix models
> #27,-0.33386,-0.51262,-0.79105,493.43,-0.74233,-0.37422,0.5558,361.76,-0.58094,0.77278,-0.25559,220.49
> fitmap #27 inMap #1
Fit molecule R_249-277.pdb (#27) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 608 atoms
average map value = 4.13, steps = 92
shifted from previous position = 4.84
rotated from previous position = 17.1 degrees
atoms outside contour = 199, contour level = 3.557
Position of R_249-277.pdb (#27) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.46057988 -0.27024761 -0.84547762 459.39257301
-0.69965708 -0.47561654 0.53316871 386.07093887
-0.54621071 0.83711119 0.02997876 154.74498674
Axis 0.50217219 -0.49444724 -0.70946812
Axis point 322.84166167 85.10951128 0.00000000
Rotation angle (degrees) 162.38449968
Shift along axis -69.98417098
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #27 models
Drag select of 285 atoms, 316 bonds, 20 residues
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-224-240.pdb
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-224-240.pdb models #21
> selectedOnly true relModel #21
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-224-240.pdb
Chain information for R-224-240.pdb #28
---
Chain | Description
A | No description available
C | No description available
> select #28/A:232
23 atoms, 25 bonds, 1 residue, 1 model selected
> show #!1 models
> view matrix models #28,1,0,0,-49.776,0,1,0,76.128,0,0,1,33.139
> ui mousemode right "rotate selected models"
> view matrix models
> #28,0.18853,-0.60536,0.7733,-14.697,-0.70458,0.46515,0.53591,141.78,-0.68412,-0.64589,-0.33884,577.93
> view matrix models
> #28,0.21861,-0.87425,0.43346,102.71,-0.76754,0.12024,0.62962,178.57,-0.60256,-0.47034,-0.64474,614.76
> view matrix models
> #28,0.4886,-0.87251,0.0015015,162.73,-0.50988,-0.28413,0.81197,146.05,-0.70802,-0.39749,-0.5837,607.6
> view matrix models
> #28,0.58621,-0.75345,0.29777,55.111,-0.55541,-0.10617,0.82477,125.5,-0.58981,-0.64888,-0.48071,597.11
> select clear
> select #28/C:320
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
44 atoms, 49 bonds, 2 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #28/A:233
20 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #28,0.58621,-0.75345,0.29777,104.55,-0.55541,-0.10617,0.82477,128.85,-0.58981,-0.64888,-0.48071,619.94
> view matrix models
> #28,0.58621,-0.75345,0.29777,111.45,-0.55541,-0.10617,0.82477,160.97,-0.58981,-0.64888,-0.48071,586.9
> view matrix models
> #28,0.58621,-0.75345,0.29777,110.32,-0.55541,-0.10617,0.82477,162.91,-0.58981,-0.64888,-0.48071,588.98
> fitmap #28 inMap #1
Fit molecule R-224-240.pdb (#28) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 388 atoms
average map value = 4.51, steps = 120
shifted from previous position = 4.48
rotated from previous position = 66.2 degrees
atoms outside contour = 79, contour level = 3.557
Position of R-224-240.pdb (#28) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.61024285 -0.35258228 -0.70942892 298.94537643
0.31792600 -0.71123189 0.62695475 148.33838204
-0.72562161 -0.60814056 -0.32192910 568.42099088
Axis -0.87878675 0.01152131 0.47707557
Axis point 0.00000000 207.78787262 330.72902833
Rotation angle (degrees) 135.35375367
Shift along axis 10.17958437
> show #27 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #21/B:32
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #21/B:33
45 atoms, 49 bonds, 2 residues, 1 model selected
> select add #21/B:34
68 atoms, 74 bonds, 3 residues, 1 model selected
> select add #21/B:35
88 atoms, 95 bonds, 4 residues, 1 model selected
> select add #21/B:57
111 atoms, 120 bonds, 5 residues, 1 model selected
> select add #21/B:56
133 atoms, 144 bonds, 6 residues, 1 model selected
> select add #21/B:55
153 atoms, 165 bonds, 7 residues, 1 model selected
> select add #21/B:54
175 atoms, 189 bonds, 8 residues, 1 model selected
> select add #21/B:53
198 atoms, 214 bonds, 9 residues, 1 model selected
> select add #21/B:52
218 atoms, 235 bonds, 10 residues, 1 model selected
> select add #21/B:51
238 atoms, 256 bonds, 11 residues, 1 model selected
> select add #21/B:50
258 atoms, 277 bonds, 12 residues, 1 model selected
> select add #21/B:49
280 atoms, 301 bonds, 13 residues, 1 model selected
> select add #21/B:48
302 atoms, 325 bonds, 14 residues, 1 model selected
> select add #21/B:47
324 atoms, 349 bonds, 15 residues, 1 model selected
> select add #21/B:46
347 atoms, 374 bonds, 16 residues, 1 model selected
> select add #21/B:45
369 atoms, 398 bonds, 17 residues, 1 model selected
> select add #21/B:44
392 atoms, 423 bonds, 18 residues, 1 model selected
> select add #21/B:43
412 atoms, 444 bonds, 19 residues, 1 model selected
> select add #21/B:42
435 atoms, 469 bonds, 20 residues, 1 model selected
> select add #21/B:41
455 atoms, 490 bonds, 21 residues, 1 model selected
> select add #21/B:40
478 atoms, 515 bonds, 22 residues, 1 model selected
> select add #21/B:39
500 atoms, 539 bonds, 23 residues, 1 model selected
> select add #21/B:38
522 atoms, 563 bonds, 24 residues, 1 model selected
> select add #21/B:37
545 atoms, 588 bonds, 25 residues, 1 model selected
> select add #21/B:36
568 atoms, 613 bonds, 26 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #27 models
Drag select of 280 atoms, 309 bonds, 18 residues
> delete atoms sel
> delete bonds sel
> show #27 models
> show #!1 models
> hide #!1 models
> select #25/A:1
23 atoms, 25 bonds, 1 residue, 1 model selected
> show #!1 models
> view matrix models
> #25,-0.98432,0.13603,-0.11229,190.73,-0.10998,0.024412,0.99363,249.38,0.1379,0.9904,-0.0090693,262.54
> fitmap #25 inMap #1
Fit molecule fold_2024_07_21_21_09_model_0.cif (#25) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 212 atoms
average map value = 4.577, steps = 64
shifted from previous position = 1.02
rotated from previous position = 0.0143 degrees
atoms outside contour = 45, contour level = 3.557
Position of fold_2024_07_21_21_09_model_0.cif (#25) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.98427820 0.13617421 -0.11248552 191.16678827
-0.11016541 0.02447990 0.99361175 248.46373434
0.13805793 0.99038241 -0.00909335 262.57611094
Axis -0.00919054 -0.71303357 -0.70106966
Axis point 93.48019577 0.00000000 20.80150922
Rotation angle (degrees) 169.88127875
Shift along axis -363.00405376
> ui mousemode right "translate selected atoms"
> select #28/A:240
23 atoms, 25 bonds, 1 residue, 1 model selected
> hide #!1 models
> show #!1 models
> select clear
> select #27/A:276
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #27/A:275
45 atoms, 49 bonds, 2 residues, 1 model selected
> select add #27/A:274
65 atoms, 70 bonds, 3 residues, 1 model selected
> select subtract #27/A:274
45 atoms, 49 bonds, 2 residues, 1 model selected
> select subtract #27/A:276
22 atoms, 24 bonds, 1 residue, 1 model selected
> select subtract #27/A:275
Nothing selected
> select add #27/A:276
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #27/A:249
43 atoms, 46 bonds, 2 residues, 1 model selected
> select clear
> select #27/A:249
20 atoms, 21 bonds, 1 residue, 1 model selected
> hide #!1 models
> select add #27/A:250
40 atoms, 42 bonds, 2 residues, 1 model selected
> show #!1 models
> select subtract #27/A:250
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #27/A:250
20 atoms, 21 bonds, 1 residue, 1 model selected
> hide #!1 models
> select add #27/A:249
40 atoms, 42 bonds, 2 residues, 1 model selected
> select subtract #27/A:250
20 atoms, 21 bonds, 1 residue, 1 model selected
> show #!1 models
> hide #!1 models
> select clear
> show #!1 models
> select #27/A:250
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #27/A:251
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add #27/A:252
65 atoms, 70 bonds, 3 residues, 1 model selected
> select add #27/A:253
88 atoms, 95 bonds, 4 residues, 1 model selected
> select subtract #27/A:253
65 atoms, 70 bonds, 3 residues, 1 model selected
> select subtract #27/A:252
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add #27/A:249
62 atoms, 66 bonds, 3 residues, 1 model selected
> select clear
> select #27/A:249
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #27/A:253
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #27/A:252
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #27/A:253
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #27/A:252
46 atoms, 50 bonds, 2 residues, 1 model selected
> select add #27/A:251
68 atoms, 74 bonds, 3 residues, 1 model selected
> select #27/A:249
20 atoms, 21 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #27/A:250
20 atoms, 21 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #27/A:253
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #27/A:252
46 atoms, 50 bonds, 2 residues, 1 model selected
> select add #27/A:251
68 atoms, 74 bonds, 3 residues, 1 model selected
> select #27/A:254
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #27/A:253
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #27/A:252
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #27/A:251
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #27/A:252
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #27/A:254
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #27/A:253
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #27/A:252
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #27/A:251
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #27/A:253
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #27/A:252
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #27/A:251
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #27/A:251
22 atoms, 24 bonds, 1 residue, 1 model selected
> ui tool show "Model Panel"
> combine #21 #22 #23 #25 #27 #28
Remapping chain ID 'D' in R-21.pdb #22 to 'E'
Remapping chain ID 'D' in R21-1.pdb #23 to 'F'
Remapping chain ID 'A' in R_249-277.pdb #27 to 'B'
Remapping chain ID 'A' in R-224-240.pdb #28 to 'G'
> hide #!21 models
> hide #22 models
> hide #23 models
> hide #25 models
> hide #27 models
> hide #28 models
> show #!2 models
> hide #!1 models
> select #2
2 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.8681,-0.49636,-0.0054412,496,0.055952,-0.086953,-0.99464,408,0.49323,-0.86375,0.10326,250.83
> view matrix models
> #2,-0.43728,0.86473,-0.24705,181.73,-0.14096,-0.33721,-0.93081,486.77,-0.88821,-0.3722,0.26935,411.27
> view matrix models
> #2,-0.18991,0.97867,0.078309,40.321,-0.63544,-0.061717,-0.76968,503.59,-0.74844,-0.19593,0.63361,272.27
> view matrix models
> #2,-0.24426,0.96946,0.021836,65.169,-0.536,-0.11621,-0.83618,506.96,-0.80811,-0.21595,0.54801,306.33
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.24426,0.96946,0.021836,84.902,-0.536,-0.11621,-0.83618,522.32,-0.80811,-0.21595,0.54801,329.55
> view matrix models
> #2,-0.24426,0.96946,0.021836,80.212,-0.536,-0.11621,-0.83618,523.43,-0.80811,-0.21595,0.54801,329.68
> view matrix models
> #2,-0.24426,0.96946,0.021836,79.228,-0.536,-0.11621,-0.83618,521.77,-0.80811,-0.21595,0.54801,329.97
> fitmap #29 inMap #2
Fit molecule combination (#29) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 12136 atoms
average map value = 4.534, steps = 216
shifted from previous position = 6.89
rotated from previous position = 17.5 degrees
atoms outside contour = 5657, contour level = 3.0813
Position of combination (#29) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
0.99999969 0.00033307 -0.00071765 0.05150646
-0.00033296 0.99999993 0.00015563 0.04534734
0.00071771 -0.00015539 0.99999973 -0.12653802
Axis -0.19286697 -0.89007017 -0.41301019
Axis point 175.20524833 0.00000000 72.22236298
Rotation angle (degrees) 0.04619864
Shift along axis 0.00196528
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-combine-new-7.pdb models
> #29 relModel #2
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/RealSpaceRefine_6/R-combine-
> new-7_real_space_refined_006.pdb
Chain information for R-combine-new-7_real_space_refined_006.pdb #30
---
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
> select #30/H:45@O2
1 atom, 1 residue, 1 model selected
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
6069 atoms, 6800 bonds, 283 residues, 1 model selected
> select up
12136 atoms, 13587 bonds, 567 residues, 1 model selected
> style sel stick
Changed 12136 atom styles
> cartoon sel
> ui mousemode right "rotate selected models"
> view matrix models
> #30,0.29014,0.74582,0.59964,-116.72,0.084308,0.60424,-0.79233,225.15,-0.95326,0.28044,0.11243,339.41
> view matrix models
> #30,0.37552,0.92503,-0.057467,-26.204,-0.34165,0.080525,-0.93637,440.99,-0.86154,0.37126,0.34628,253.41
> view matrix models
> #30,-0.19245,0.9604,-0.20148,117.11,-0.0074181,-0.20674,-0.97837,432.63,-0.98128,-0.18679,0.046912,444.75
> ui mousemode right "translate selected models"
> view matrix models
> #30,-0.19245,0.9604,-0.20148,109.72,-0.0074181,-0.20674,-0.97837,453.92,-0.98128,-0.18679,0.046912,448.6
> view matrix models
> #30,-0.19245,0.9604,-0.20148,113.68,-0.0074181,-0.20674,-0.97837,454.82,-0.98128,-0.18679,0.046912,457.79
> fitmap #30 inMap #2
Fit molecule R-combine-new-7_real_space_refined_006.pdb (#30) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 12136 atoms
average map value = 4.856, steps = 308
shifted from previous position = 9.42
rotated from previous position = 32.9 degrees
atoms outside contour = 5066, contour level = 3.0813
Position of R-combine-new-7_real_space_refined_006.pdb (#30) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
0.99999998 -0.00007985 -0.00020629 0.04532712
0.00007991 0.99999995 0.00030025 -0.06461344
0.00020627 -0.00030026 0.99999993 0.00824178
Axis -0.80509561 -0.55311902 0.21419715
Axis point 0.00000000 26.67958032 213.34072968
Rotation angle (degrees) 0.02136818
Shift along axis 0.00101163
> hide #!29 models
> select clear
> select #30/H:552
22 atoms, 24 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!30 models
> hide #!2 models
> show #19 models
> select #19/B:545
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #19/B:546
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add #19/B:547
65 atoms, 70 bonds, 3 residues, 1 model selected
> select add #19/B:548
88 atoms, 95 bonds, 4 residues, 1 model selected
> select add #19/B:549
110 atoms, 119 bonds, 5 residues, 1 model selected
> select add #19/B:550
133 atoms, 144 bonds, 6 residues, 1 model selected
> select add #19/B:551
153 atoms, 165 bonds, 7 residues, 1 model selected
> select add #19/B:552
175 atoms, 189 bonds, 8 residues, 1 model selected
> select add #19/B:553
197 atoms, 213 bonds, 9 residues, 1 model selected
> select add #19/B:554
219 atoms, 237 bonds, 10 residues, 1 model selected
> select add #19/B:555
241 atoms, 261 bonds, 11 residues, 1 model selected
> select add #19/B:556
264 atoms, 286 bonds, 12 residues, 1 model selected
> select add #19/B:557
284 atoms, 307 bonds, 13 residues, 1 model selected
> select add #19/B:558
304 atoms, 328 bonds, 14 residues, 1 model selected
> select add #19/B:559
324 atoms, 349 bonds, 15 residues, 1 model selected
> select subtract #19/B:559
304 atoms, 328 bonds, 14 residues, 1 model selected
> select ~sel & ##selected
12042 atoms, 13491 bonds, 564 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> ui tool show "Model Panel"
> close #5
> close #6
> close #8
> close #4
> close #9
> close #3
> close #20
> close #21
> close #22-23#24
> close #27-28#29
> show #!30 models
> show #!2 models
> hide #19 models
> show #19 models
> hide #!30 models
> show #!30 models
> select clear
> select #19/B:548
23 atoms, 25 bonds, 1 residue, 1 model selected
> view matrix models #19,1,0,0,272.16,0,1,0,54.563,0,0,1,86.053
> view matrix models #19,1,0,0,192.01,0,1,0,150.79,0,0,1,280.78
> view matrix models #19,1,0,0,189.47,0,1,0,161.83,0,0,1,247.53
> view matrix models #19,1,0,0,235.73,0,1,0,239.22,0,0,1,202.75
> hide #!2 models
> ui mousemode right "rotate selected models"
> view matrix models
> #19,-0.15176,0.90128,-0.40579,295.92,0.77442,-0.14668,-0.61543,184.92,-0.6142,-0.40765,-0.67571,212.26
> view matrix models
> #19,0.20481,0.17673,-0.96271,266.7,-0.47869,-0.83983,-0.25602,259.76,-0.85376,0.51328,-0.087406,235.67
> view matrix models
> #19,-0.2402,0.25771,-0.93589,292.34,-0.22566,-0.95253,-0.20438,246.09,-0.94413,0.1621,0.28695,245.86
> view matrix models
> #19,-0.59624,-0.22399,0.77093,336.75,-0.11371,-0.92704,-0.35729,237.74,0.79471,-0.3007,0.52727,150.81
> ui mousemode right "translate selected models"
> view matrix models
> #19,-0.59624,-0.22399,0.77093,326.18,-0.11371,-0.92704,-0.35729,224.76,0.79471,-0.3007,0.52727,157.14
> ui mousemode right "rotate selected models"
> view matrix models
> #19,-0.66767,0.72959,-0.14805,317.88,-0.69803,-0.5444,0.46517,270.51,0.25879,0.41392,0.87275,193.57
> view matrix models
> #19,0.43952,0.69876,-0.56441,249.54,-0.89801,0.35581,-0.2588,272.58,0.019988,0.6206,0.78388,206.02
> view matrix models
> #19,0.50983,0.85863,-0.053099,253.42,-0.18573,0.049593,-0.98135,221.48,-0.83998,0.51019,0.18476,245.36
> view matrix models
> #19,0.0092013,0.63097,-0.77576,270.69,-0.12103,-0.76938,-0.62722,221.81,-0.99261,0.099663,0.069288,251.68
> view matrix models
> #19,0.34562,0.57687,-0.74011,252.18,-0.40591,-0.6192,-0.67218,237.4,-0.84604,0.53274,0.02015,243.24
> ui mousemode right "translate selected models"
> view matrix models
> #19,0.34562,0.57687,-0.74011,226.49,-0.40591,-0.6192,-0.67218,253.79,-0.84604,0.53274,0.02015,249.5
> view matrix models
> #19,0.34562,0.57687,-0.74011,231.13,-0.40591,-0.6192,-0.67218,257.78,-0.84604,0.53274,0.02015,246.33
> ui mousemode right "rotate selected models"
> view matrix models
> #19,-0.24338,-0.066931,-0.96762,260.08,-0.78392,-0.57391,0.23687,292.62,-0.57118,0.81618,0.087211,232.19
> ui mousemode right "translate selected models"
> view matrix models
> #19,-0.24338,-0.066931,-0.96762,262.34,-0.78392,-0.57391,0.23687,293.68,-0.57118,0.81618,0.087211,235.86
> view matrix models
> #19,-0.24338,-0.066931,-0.96762,258.16,-0.78392,-0.57391,0.23687,295.71,-0.57118,0.81618,0.087211,236.3
> view matrix models
> #19,-0.24338,-0.066931,-0.96762,257.31,-0.78392,-0.57391,0.23687,296.88,-0.57118,0.81618,0.087211,236.21
> show #!1 models
> hide #!1 models
> show #!2 models
> fitmap #19 inMap #2
Fit molecule fold_r_e_m_model_4.cif (#19) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 304 atoms
average map value = 6.072, steps = 56
shifted from previous position = 2.87
rotated from previous position = 11.7 degrees
atoms outside contour = 67, contour level = 3.0813
Position of fold_r_e_m_model_4.cif (#19) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
0.90559455 -0.40278986 0.13288663 154.17129879
0.12132778 -0.05420770 -0.99113122 212.43610847
0.40642108 0.91368587 -0.00022060 137.50758412
Axis 0.95505670 -0.13714750 0.26278747
Axis point 0.00000000 70.16605908 161.04879179
Rotation angle (degrees) 94.26771815
Shift along axis 154.24252073
> hide #!2 models
> select clear
> select #30/H:558
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #30/H:557
40 atoms, 42 bonds, 2 residues, 1 model selected
> select add #30/H:556
63 atoms, 67 bonds, 3 residues, 1 model selected
> select add #30/H:555
85 atoms, 91 bonds, 4 residues, 1 model selected
> select add #30/H:554@C4'
86 atoms, 91 bonds, 5 residues, 1 model selected
> select add #30/H:553
108 atoms, 115 bonds, 6 residues, 1 model selected
> select add #30/H:551
128 atoms, 136 bonds, 7 residues, 1 model selected
> select add #30/H:550
151 atoms, 161 bonds, 8 residues, 1 model selected
> select add #30/H:549
173 atoms, 185 bonds, 9 residues, 1 model selected
> select add #30/H:548
196 atoms, 210 bonds, 10 residues, 1 model selected
> select add #30/H:547
219 atoms, 235 bonds, 11 residues, 1 model selected
> select add #19/B:547
242 atoms, 260 bonds, 12 residues, 2 models selected
> select subtract #19/B:547
219 atoms, 235 bonds, 11 residues, 1 model selected
> select add #30/H:546
241 atoms, 259 bonds, 12 residues, 1 model selected
> select add #30/H:545
261 atoms, 280 bonds, 13 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> combine #19 #30
Remapping chain ID 'B' in R-combine-new-7_real_space_refined_006.pdb #30 to
'I'
> hide #19 models
> hide #!30 models
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-combine-new-8.pdb models #3
> relModel #2
> show #!2 models
> fitmap #3 inMap #2
Fit molecule combination (#3) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 12157 atoms
average map value = 4.833, steps = 72
shifted from previous position = 0.0145
rotated from previous position = 0.00778 degrees
atoms outside contour = 5106, contour level = 3.0813
Position of combination (#3) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
0.90556539 -0.40282720 0.13297207 154.16586673
0.12136748 -0.05432863 -0.99111974 212.42797707
0.40647418 0.91366222 -0.00030800 137.51280283
Axis 0.95504758 -0.13713251 0.26282844
Axis point 0.00000000 70.16681139 161.03141023
Rotation angle (degrees) 94.27454059
Shift along axis 154.24723228
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-combine-new-8.pdb models #3
> relModel #2
> show #19 models
> hide #19 models
> show #!18 models
> hide #!3 models
> close #18
> show #15 models
> show #!16 models
> hide #15 models
> close #16
> show #7 models
> select #7/A:545
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #7/A:175
40 atoms, 42 bonds, 2 residues, 1 model selected
> select add #7/A:174
63 atoms, 67 bonds, 3 residues, 1 model selected
> select add #7/A:544
86 atoms, 92 bonds, 4 residues, 1 model selected
> select add #7/A:176
109 atoms, 117 bonds, 5 residues, 1 model selected
> select add #7/A:177
132 atoms, 142 bonds, 6 residues, 1 model selected
> select add #7/A:543
154 atoms, 166 bonds, 7 residues, 1 model selected
> select add #7/A:542
176 atoms, 190 bonds, 8 residues, 1 model selected
> select add #7/A:541
199 atoms, 215 bonds, 9 residues, 1 model selected
> select add #7/A:540
219 atoms, 236 bonds, 10 residues, 1 model selected
> select add #7/A:539
241 atoms, 260 bonds, 11 residues, 1 model selected
> select add #7/A:538
261 atoms, 281 bonds, 12 residues, 1 model selected
> select add #7/A:538
261 atoms, 281 bonds, 12 residues, 1 model selected
> select add #7/A:537
284 atoms, 306 bonds, 13 residues, 1 model selected
> select add #7/A:536
304 atoms, 327 bonds, 14 residues, 1 model selected
> select add #7/A:178
326 atoms, 351 bonds, 15 residues, 1 model selected
> select add #7/A:179
349 atoms, 376 bonds, 16 residues, 1 model selected
> select add #7/A:180
369 atoms, 397 bonds, 17 residues, 1 model selected
> select add #7/A:181
392 atoms, 422 bonds, 18 residues, 1 model selected
> select add #7/A:182
412 atoms, 443 bonds, 19 residues, 1 model selected
> select add #7/A:183
434 atoms, 467 bonds, 20 residues, 1 model selected
> select add #7/A:184
454 atoms, 488 bonds, 21 residues, 1 model selected
> select add #7/A:185
476 atoms, 512 bonds, 22 residues, 1 model selected
> select add #7/A:535
499 atoms, 537 bonds, 23 residues, 1 model selected
> select add #7/A:534
519 atoms, 558 bonds, 24 residues, 1 model selected
> select add #7/A:533
542 atoms, 583 bonds, 25 residues, 1 model selected
> select add #7/A:532
564 atoms, 607 bonds, 26 residues, 1 model selected
> select add #7/A:531
587 atoms, 632 bonds, 27 residues, 1 model selected
> select add #7/A:76
609 atoms, 656 bonds, 28 residues, 1 model selected
> select subtract #7/A:76
587 atoms, 632 bonds, 27 residues, 1 model selected
> select add #7/A:530
607 atoms, 653 bonds, 28 residues, 1 model selected
> select add #7/A:529
630 atoms, 678 bonds, 29 residues, 1 model selected
> select add #7/A:528
652 atoms, 702 bonds, 30 residues, 1 model selected
> select add #7/A:526
675 atoms, 727 bonds, 31 residues, 1 model selected
> select add #7/A:527
695 atoms, 748 bonds, 32 residues, 1 model selected
> select add #7/A:186
715 atoms, 769 bonds, 33 residues, 1 model selected
> select add #7/A:187
738 atoms, 794 bonds, 34 residues, 1 model selected
> select add #7/A:188
761 atoms, 819 bonds, 35 residues, 1 model selected
> select add #7/A:189
783 atoms, 843 bonds, 36 residues, 1 model selected
> select add #7/A:190
803 atoms, 864 bonds, 37 residues, 1 model selected
> select add #7/A:191
823 atoms, 885 bonds, 38 residues, 1 model selected
> select add #7/A:192
846 atoms, 910 bonds, 39 residues, 1 model selected
> select add #7/A:525
866 atoms, 931 bonds, 40 residues, 1 model selected
> select add #7/A:524
888 atoms, 955 bonds, 41 residues, 1 model selected
> select add #7/A:193
908 atoms, 976 bonds, 42 residues, 1 model selected
> select subtract #7/A:346
908 atoms, 976 bonds, 42 residues, 1 model selected
> select add #7/A:194
930 atoms, 1000 bonds, 43 residues, 1 model selected
> select add #7/A:195
952 atoms, 1024 bonds, 44 residues, 1 model selected
> select add #7/A:196
975 atoms, 1049 bonds, 45 residues, 1 model selected
> select add #7/A:197
998 atoms, 1074 bonds, 46 residues, 1 model selected
> select add #7/A:198
1018 atoms, 1095 bonds, 47 residues, 1 model selected
> select add #7/A:199
1040 atoms, 1119 bonds, 48 residues, 1 model selected
> select subtract #7/A:199
1018 atoms, 1095 bonds, 47 residues, 1 model selected
> select add #7/A:519
1040 atoms, 1119 bonds, 48 residues, 1 model selected
> select add #7/A:520
1060 atoms, 1140 bonds, 49 residues, 1 model selected
> select add #7/A:521
1080 atoms, 1161 bonds, 50 residues, 1 model selected
> select add #7/A:522
1103 atoms, 1186 bonds, 51 residues, 1 model selected
> select add #7/A:523
1125 atoms, 1210 bonds, 52 residues, 1 model selected
> select add #7/A:518
1148 atoms, 1235 bonds, 53 residues, 1 model selected
> select add #7/A:517
1168 atoms, 1256 bonds, 54 residues, 1 model selected
> select add #7/A:516
1191 atoms, 1281 bonds, 55 residues, 1 model selected
> select add #7/A:515
1211 atoms, 1302 bonds, 56 residues, 1 model selected
> view matrix models #7,1,0,0,2.2735,0,1,0,2.2992,0,0,1,-1.7424
> select ~sel & ##selected
11134 atoms, 12476 bonds, 521 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!2 models
> select #7/A:528
22 atoms, 24 bonds, 1 residue, 1 model selected
> view matrix models #7,1,0,0,127.23,0,1,0,229.92,0,0,1,-15.073
> view matrix models #7,1,0,0,269.68,0,1,0,129.86,0,0,1,179.9
> view matrix models #7,1,0,0,270.52,0,1,0,214.69,0,0,1,203.03
> view matrix models #7,1,0,0,281.23,0,1,0,213.54,0,0,1,212.45
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.16182,0.97199,0.17044,236.05,-0.98283,-0.14322,-0.11635,194.17,-0.088685,-0.18634,0.97847,211.5
> view matrix models
> #7,-0.81527,-0.50332,0.28638,229.61,0.47003,-0.28628,0.83494,238.88,-0.33825,0.8153,0.46997,195.14
> view matrix models
> #7,-0.78176,-0.066011,-0.62008,227.86,-0.32829,-0.80186,0.49925,219.62,-0.53017,0.59386,0.60519,191.11
> view matrix models
> #7,0.52131,-0.31011,-0.79503,270.56,-0.59328,-0.80136,-0.076444,212.3,-0.61339,0.51153,-0.60174,191.09
> view matrix models
> #7,0.93031,0.10759,0.35065,277.56,0.23889,-0.90317,-0.35667,239.31,0.27832,0.41558,-0.86593,219.86
> view matrix models
> #7,-0.48999,-0.041808,0.87072,234.44,0.60609,-0.73425,0.30582,248.06,0.62654,0.67759,0.38512,226.29
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.48999,-0.041808,0.87072,228.73,0.60609,-0.73425,0.30582,246.43,0.62654,0.67759,0.38512,236.64
> fitmap #7 inMap #2
Fit molecule fold_r_e_model_0.cif (#7) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 1211 atoms
average map value = 3.936, steps = 308
shifted from previous position = 5.18
rotated from previous position = 20.5 degrees
atoms outside contour = 574, contour level = 3.0813
Position of fold_r_e_model_0.cif (#7) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
-0.55176898 -0.22561714 -0.80289968 190.08039980
-0.83398172 0.14343865 0.53282252 194.77034322
-0.00504704 0.96359860 -0.26730557 187.45468828
Axis 0.39451993 -0.73070159 -0.55716175
Axis point 128.96993918 0.00000000 71.88439885
Rotation angle (degrees) 146.91041277
Shift along axis -171.77107506
> show #!30 models
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-combine-new-8-coot-0.pdb
Chain information for R-combine-new-8-coot-0.pdb #4
---
Chain | Description
A | 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
> close #30
> select #4/H:66@P
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
6046 atoms, 6774 bonds, 282 residues, 1 model selected
> select up
12113 atoms, 13561 bonds, 566 residues, 1 model selected
> style sel stick
Changed 12113 atom styles
> cartoon sel
> select #4/H:75
23 atoms, 25 bonds, 1 residue, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.60062,0.56271,0.568,109.88,-0.38985,0.41413,-0.82251,365.59,-0.69805,-0.71545,-0.02936,498.24
> view matrix models
> #4,-0.23374,0.96387,-0.12775,109.3,-0.48945,-0.23017,-0.8411,507.95,-0.84012,-0.13407,0.52557,302.25
> view matrix models
> #4,-0.032216,0.99314,-0.1124,58.476,-0.44156,-0.11503,-0.88983,487.37,-0.89665,0.020965,0.44224,303.67
> view matrix models
> #4,-0.011842,0.97693,-0.21324,78.856,-0.026079,-0.21348,-0.9766,437.08,-0.99959,-0.006004,0.028005,419.21
> view matrix models
> #4,0.17872,0.98355,0.026145,-13.682,-0.43615,0.10302,-0.89396,447.27,-0.88195,0.14837,0.44739,276.29
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.17872,0.98355,0.026145,-14.101,-0.43615,0.10302,-0.89396,447.33,-0.88195,0.14837,0.44739,297.13
> view matrix models
> #4,0.17872,0.98355,0.026145,-17.172,-0.43615,0.10302,-0.89396,463.59,-0.88195,0.14837,0.44739,294.73
> fitmap #4 inMap #2
Fit molecule R-combine-new-8-coot-0.pdb (#4) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 12113 atoms
average map value = 4.876, steps = 248
shifted from previous position = 9.72
rotated from previous position = 25.5 degrees
atoms outside contour = 5024, contour level = 3.0813
Position of R-combine-new-8-coot-0.pdb (#4) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 -0.00008287 -0.00001579 0.01443366
0.00008287 1.00000000 -0.00000461 -0.01996177
0.00001579 0.00000461 1.00000000 0.00342560
Axis 0.05451300 -0.18695372 0.98085506
Axis point 223.12489126 168.98868431 0.00000000
Rotation angle (degrees) 0.00484052
Shift along axis 0.00787876
> hide #!2 models
> view matrix models
> #4,-0.24418,0.96948,0.021836,79.143,-0.53602,-0.11617,-0.83617,522.14,-0.80812,-0.21588,0.54803,330.02
> combine #4 #7
Remapping chain ID 'A' in fold_r_e_model_0.cif #7 to 'B'
> hide #!7 models
> hide #!4 models
> show #!2 models
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-combine-new-9.pdb models #5
> relModel #5
> select #5/B:515
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #5/B:516
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add #5/B:517
63 atoms, 67 bonds, 3 residues, 1 model selected
> select add #5/B:518
86 atoms, 92 bonds, 4 residues, 1 model selected
> select add #5/B:519
108 atoms, 116 bonds, 5 residues, 1 model selected
> select add #5/B:520
128 atoms, 137 bonds, 6 residues, 1 model selected
> select add #5/B:521
148 atoms, 158 bonds, 7 residues, 1 model selected
> select add #5/B:522
171 atoms, 183 bonds, 8 residues, 1 model selected
> select add #5/B:523
193 atoms, 207 bonds, 9 residues, 1 model selected
> select add #5/B:524
215 atoms, 231 bonds, 10 residues, 1 model selected
> select add #5/B:525
235 atoms, 252 bonds, 11 residues, 1 model selected
> select subtract #5/B:525
215 atoms, 231 bonds, 10 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #5/B:198
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #5/B:197
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add #5/B:196
66 atoms, 71 bonds, 3 residues, 1 model selected
> select add #5/B:195
88 atoms, 95 bonds, 4 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #5/C:445
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #5/C:446
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add #5/C:447
66 atoms, 71 bonds, 3 residues, 1 model selected
> select add #5/C:444
86 atoms, 92 bonds, 4 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #5/C:443
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #5/C:442
42 atoms, 45 bonds, 2 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!7 models
> hide #!7 models
> show #10 models
> hide #!5 models
> select #10/A:433
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #10/A:434
40 atoms, 42 bonds, 2 residues, 1 model selected
> select add #10/A:435
63 atoms, 67 bonds, 3 residues, 1 model selected
> select add #10/A:436
83 atoms, 88 bonds, 4 residues, 1 model selected
> select add #10/A:437
103 atoms, 109 bonds, 5 residues, 1 model selected
> select add #10/A:438
125 atoms, 133 bonds, 6 residues, 1 model selected
> select add #10/A:439
148 atoms, 158 bonds, 7 residues, 1 model selected
> select add #10/A:440
168 atoms, 179 bonds, 8 residues, 1 model selected
> select add #10/A:441
188 atoms, 200 bonds, 9 residues, 1 model selected
> select add #10/A:442
210 atoms, 224 bonds, 10 residues, 1 model selected
> select add #10/A:443
230 atoms, 245 bonds, 11 residues, 1 model selected
> select add #10/A:444
250 atoms, 266 bonds, 12 residues, 1 model selected
> select add #10/A:445
273 atoms, 291 bonds, 13 residues, 1 model selected
> select add #10/A:446
293 atoms, 312 bonds, 14 residues, 1 model selected
> select add #10/A:447
316 atoms, 337 bonds, 15 residues, 1 model selected
> select add #10/A:448
336 atoms, 358 bonds, 16 residues, 1 model selected
> select add #10/A:449
356 atoms, 379 bonds, 17 residues, 1 model selected
> select add #10/A:450
378 atoms, 403 bonds, 18 residues, 1 model selected
> select add #10/A:452
400 atoms, 427 bonds, 19 residues, 1 model selected
> select add #10/A:451
423 atoms, 452 bonds, 20 residues, 1 model selected
> select add #10/A:453
443 atoms, 473 bonds, 21 residues, 1 model selected
> select add #10/A:454
463 atoms, 494 bonds, 22 residues, 1 model selected
> select add #10/A:455
485 atoms, 518 bonds, 23 residues, 1 model selected
> select add #10/A:456
505 atoms, 539 bonds, 24 residues, 1 model selected
> select add #10/A:457
527 atoms, 563 bonds, 25 residues, 1 model selected
> select add #10/A:458
547 atoms, 584 bonds, 26 residues, 1 model selected
> select add #10/A:459
569 atoms, 608 bonds, 27 residues, 1 model selected
> select add #10/A:460
589 atoms, 629 bonds, 28 residues, 1 model selected
> select add #10/A:461
609 atoms, 650 bonds, 29 residues, 1 model selected
> select add #10/A:462
631 atoms, 674 bonds, 30 residues, 1 model selected
> select add #10/A:463
653 atoms, 698 bonds, 31 residues, 1 model selected
> select add #10/A:464
675 atoms, 722 bonds, 32 residues, 1 model selected
> select add #10/A:465
697 atoms, 746 bonds, 33 residues, 1 model selected
> select add #10/A:466
720 atoms, 771 bonds, 34 residues, 1 model selected
> select add #10/A:517
740 atoms, 792 bonds, 35 residues, 1 model selected
> select add #10/A:516
763 atoms, 817 bonds, 36 residues, 1 model selected
> select add #10/A:515
783 atoms, 838 bonds, 37 residues, 1 model selected
> select add #10/A:514
805 atoms, 862 bonds, 38 residues, 1 model selected
> select add #10/A:513
825 atoms, 883 bonds, 39 residues, 1 model selected
> select add #10/A:512
848 atoms, 908 bonds, 40 residues, 1 model selected
> select add #10/A:511
871 atoms, 933 bonds, 41 residues, 1 model selected
> select add #10/A:510
894 atoms, 958 bonds, 42 residues, 1 model selected
> select add #10/A:468
916 atoms, 982 bonds, 43 residues, 1 model selected
> select add #10/A:467
936 atoms, 1003 bonds, 44 residues, 1 model selected
> select add #10/A:509
956 atoms, 1024 bonds, 45 residues, 1 model selected
> select ~sel & ##selected
11389 atoms, 12765 bonds, 532 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!2 models
> select clear
> select #10/A:436
20 atoms, 21 bonds, 1 residue, 1 model selected
> view matrix models #10,1,0,0,231.99,0,1,0,197.46,0,0,1,176.46
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.95619,-0.21051,0.20341,231.91,-0.1617,0.1994,0.96648,192.06,-0.24402,-0.95704,0.15663,222.03
> view matrix models
> #10,0.13962,-0.92043,0.36514,230.68,-0.93395,0.00011977,0.35741,196.97,-0.32901,-0.39092,-0.85961,230.02
> view matrix models
> #10,0.3683,-0.71928,0.58905,223.82,-0.3955,-0.69462,-0.60091,255.16,0.84139,-0.011656,-0.5403,236.26
> view matrix models
> #10,0.044075,-0.33159,0.94239,195.55,0.13347,-0.9329,-0.33449,267.08,0.99007,0.14053,0.0031405,220.62
> view matrix models
> #10,0.23843,-0.5955,0.76716,212.51,-0.17946,-0.80335,-0.56782,262.38,0.95444,-0.0022849,-0.29841,232.07
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.23843,-0.5955,0.76716,263.23,-0.17946,-0.80335,-0.56782,202.87,0.95444,-0.0022849,-0.29841,257.13
> view matrix models
> #10,0.23843,-0.5955,0.76716,262.26,-0.17946,-0.80335,-0.56782,208.21,0.95444,-0.0022849,-0.29841,266.36
> view matrix models
> #10,0.23843,-0.5955,0.76716,263.14,-0.17946,-0.80335,-0.56782,208.51,0.95444,-0.0022849,-0.29841,264.14
> fitmap #10 inMap #2
Fit molecule fold_r_e_model_0.cif (#10) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 956 atoms
average map value = 3.881, steps = 180
shifted from previous position = 6.45
rotated from previous position = 35.5 degrees
atoms outside contour = 474, contour level = 3.0813
Position of fold_r_e_model_0.cif (#10) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
-0.97275766 0.23177115 -0.00496658 190.83322315
-0.15293732 -0.62549220 0.76509456 236.27013058
0.17422029 0.74501117 0.64389879 203.37807884
Axis -0.04726984 -0.42174824 -0.90547997
Axis point 96.79875530 60.27026621 0.00000000
Rotation angle (degrees) 167.73500286
Shift along axis -292.82194529
> show #!4 models
> show #!7 models
> hide #!2 models
> select #4/C:441
20 atoms, 21 bonds, 1 residue, 1 model selected
> select subtract #10/A:443
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #4/C:443
40 atoms, 42 bonds, 2 residues, 1 model selected
> select add #4/C:442
62 atoms, 66 bonds, 3 residues, 1 model selected
> select add #4/C:444
82 atoms, 87 bonds, 4 residues, 1 model selected
> select add #4/C:445
105 atoms, 112 bonds, 5 residues, 1 model selected
> select subtract #4/C:445
82 atoms, 87 bonds, 4 residues, 1 model selected
> select add #4/C:445
105 atoms, 112 bonds, 5 residues, 1 model selected
> select add #4/C:446
125 atoms, 133 bonds, 6 residues, 1 model selected
> select add #4/C:447
148 atoms, 158 bonds, 7 residues, 1 model selected
> select add #4/C:448
168 atoms, 179 bonds, 8 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #7/A:522
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #7/A:521
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add #7/A:520
63 atoms, 67 bonds, 3 residues, 1 model selected
> select add #7/A:523
85 atoms, 91 bonds, 4 residues, 1 model selected
> select add #7/A:524
107 atoms, 115 bonds, 5 residues, 1 model selected
> select add #7/A:525
127 atoms, 136 bonds, 6 residues, 1 model selected
> select add #7/A:519
149 atoms, 160 bonds, 7 residues, 1 model selected
> select add #7/A:193
169 atoms, 181 bonds, 8 residues, 1 model selected
> select subtract #7/A:193
149 atoms, 160 bonds, 7 residues, 1 model selected
> select add #7/A:518
172 atoms, 185 bonds, 8 residues, 1 model selected
> select add #7/A:517
192 atoms, 206 bonds, 9 residues, 1 model selected
> select add #7/A:516
215 atoms, 231 bonds, 10 residues, 1 model selected
> select add #7/A:515
235 atoms, 252 bonds, 11 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #4/C:516
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #4/C:515
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add #4/C:514
65 atoms, 70 bonds, 3 residues, 1 model selected
> select add #4/C:513
85 atoms, 91 bonds, 4 residues, 1 model selected
> select add #4/C:512
108 atoms, 116 bonds, 5 residues, 1 model selected
> select add #4/C:511
131 atoms, 141 bonds, 6 residues, 1 model selected
> select add #4/C:510
154 atoms, 166 bonds, 7 residues, 1 model selected
> select add #4/C:509
174 atoms, 187 bonds, 8 residues, 1 model selected
> select #10/A:449
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #4/C:439
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #10/A:449
43 atoms, 46 bonds, 2 residues, 2 models selected
> select add #10/A:440
63 atoms, 67 bonds, 3 residues, 2 models selected
> select subtract #4/C:439@C4'
62 atoms, 64 bonds, 3 residues, 2 models selected
> select subtract #4/C:439
40 atoms, 42 bonds, 2 residues, 1 model selected
> select subtract #10/A:440
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #4/C:432@N3
21 atoms, 21 bonds, 2 residues, 2 models selected
> select subtract #4/C:432
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #10/A:439
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add #10/A:450
65 atoms, 70 bonds, 3 residues, 1 model selected
> hide #!4 models
> select add #10/A:451
88 atoms, 95 bonds, 4 residues, 1 model selected
> select add #10/A:452
110 atoms, 119 bonds, 5 residues, 1 model selected
> select add #10/A:453
130 atoms, 140 bonds, 6 residues, 1 model selected
> select add #10/A:438
152 atoms, 164 bonds, 7 residues, 1 model selected
> select add #10/A:437
172 atoms, 185 bonds, 8 residues, 1 model selected
> select add #10/A:436
192 atoms, 206 bonds, 9 residues, 1 model selected
> select subtract #10/A:436
172 atoms, 185 bonds, 8 residues, 1 model selected
> select add #10/A:436
192 atoms, 206 bonds, 9 residues, 1 model selected
> select add #10/A:435
215 atoms, 231 bonds, 10 residues, 1 model selected
> select add #10/A:434
235 atoms, 252 bonds, 11 residues, 1 model selected
> select add #10/A:433
255 atoms, 273 bonds, 12 residues, 1 model selected
> select add #10/A:454
275 atoms, 294 bonds, 13 residues, 1 model selected
> select add #10/A:455
297 atoms, 318 bonds, 14 residues, 1 model selected
> select add #10/A:456
317 atoms, 339 bonds, 15 residues, 1 model selected
> select add #10/A:457
339 atoms, 363 bonds, 16 residues, 1 model selected
> select add #10/A:517
359 atoms, 384 bonds, 17 residues, 1 model selected
> select add #10/A:516
382 atoms, 409 bonds, 18 residues, 1 model selected
> select add #10/A:515
402 atoms, 430 bonds, 19 residues, 1 model selected
> select add #10/A:514
424 atoms, 454 bonds, 20 residues, 1 model selected
> select add #10/A:513
444 atoms, 475 bonds, 21 residues, 1 model selected
> select subtract #10/A:513
424 atoms, 454 bonds, 20 residues, 1 model selected
> select add #10/A:513
444 atoms, 475 bonds, 21 residues, 1 model selected
> select add #10/A:510
513 atoms, 500 bonds, 24 residues, 1 model selected
> select add #10/A:458
533 atoms, 521 bonds, 25 residues, 1 model selected
> select add #10/A:459
555 atoms, 545 bonds, 26 residues, 1 model selected
> select add #10/A:460
575 atoms, 566 bonds, 27 residues, 1 model selected
> select add #10/A:461
595 atoms, 587 bonds, 28 residues, 1 model selected
> select add #10/A:462
617 atoms, 611 bonds, 29 residues, 1 model selected
> select add #10/A:463
639 atoms, 635 bonds, 30 residues, 1 model selected
> select add #10/A:464
661 atoms, 659 bonds, 31 residues, 1 model selected
> select add #10/A:465
683 atoms, 683 bonds, 32 residues, 1 model selected
> select add #10/A:466
706 atoms, 708 bonds, 33 residues, 1 model selected
> select add #10/A:467
726 atoms, 729 bonds, 34 residues, 1 model selected
> select add #10/A:468
748 atoms, 753 bonds, 35 residues, 1 model selected
> select add #10/A:509
768 atoms, 774 bonds, 36 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!2 models
> show #!5 models
> select add #5/C:441
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #5/C:440
40 atoms, 42 bonds, 2 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #5/C:448
20 atoms, 21 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!7 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> select #5/H:174
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #5/H:175
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add #5/H:176
66 atoms, 71 bonds, 3 residues, 1 model selected
> select add #5/H:177
89 atoms, 96 bonds, 4 residues, 1 model selected
> select add #5/H:178
111 atoms, 120 bonds, 5 residues, 1 model selected
> select add #5/H:179
134 atoms, 145 bonds, 6 residues, 1 model selected
> select add #5/H:180
154 atoms, 166 bonds, 7 residues, 1 model selected
> select add #5/H:181
177 atoms, 191 bonds, 8 residues, 1 model selected
> select add #5/H:182
197 atoms, 212 bonds, 9 residues, 1 model selected
> select add #5/H:183
219 atoms, 236 bonds, 10 residues, 1 model selected
> select add #5/H:184
239 atoms, 257 bonds, 11 residues, 1 model selected
> select add #5/B:186
259 atoms, 278 bonds, 12 residues, 1 model selected
> select subtract #5/B:186
239 atoms, 257 bonds, 11 residues, 1 model selected
> select add #5/H:185
261 atoms, 281 bonds, 12 residues, 1 model selected
> select add #5/H:186
281 atoms, 302 bonds, 13 residues, 1 model selected
> select add #5/H:187
304 atoms, 327 bonds, 14 residues, 1 model selected
> select add #5/H:188
326 atoms, 351 bonds, 15 residues, 1 model selected
> select add #5/H:189
346 atoms, 372 bonds, 16 residues, 1 model selected
> select add #5/H:190
366 atoms, 393 bonds, 17 residues, 1 model selected
> select add #5/H:191
388 atoms, 417 bonds, 18 residues, 1 model selected
> select add #5/H:192
408 atoms, 438 bonds, 19 residues, 1 model selected
> select add #5/H:193
430 atoms, 462 bonds, 20 residues, 1 model selected
> select add #5/H:194
452 atoms, 486 bonds, 21 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #5/H:525
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #5/H:524
44 atoms, 48 bonds, 2 residues, 1 model selected
> select add #5/H:523
67 atoms, 73 bonds, 3 residues, 1 model selected
> select add #5/H:526
90 atoms, 98 bonds, 4 residues, 1 model selected
> select add #5/H:527
110 atoms, 119 bonds, 5 residues, 1 model selected
> select add #5/H:528
132 atoms, 143 bonds, 6 residues, 1 model selected
> select add #5/H:529
155 atoms, 168 bonds, 7 residues, 1 model selected
> select add #5/H:530
175 atoms, 189 bonds, 8 residues, 1 model selected
> select add #5/H:531
198 atoms, 214 bonds, 9 residues, 1 model selected
> select add #5/H:532
220 atoms, 238 bonds, 10 residues, 1 model selected
> select add #5/H:533
243 atoms, 263 bonds, 11 residues, 1 model selected
> select add #5/H:534
263 atoms, 284 bonds, 12 residues, 1 model selected
> select add #5/H:535
286 atoms, 309 bonds, 13 residues, 1 model selected
> select add #5/H:536
306 atoms, 330 bonds, 14 residues, 1 model selected
> select add #5/H:537
329 atoms, 355 bonds, 15 residues, 1 model selected
> select add #5/H:538
349 atoms, 376 bonds, 16 residues, 1 model selected
> select add #5/H:539
371 atoms, 400 bonds, 17 residues, 1 model selected
> select add #5/H:540
391 atoms, 421 bonds, 18 residues, 1 model selected
> select add #5/H:541
414 atoms, 446 bonds, 19 residues, 1 model selected
> select add #5/H:542
436 atoms, 470 bonds, 20 residues, 1 model selected
> select add #5/H:543
458 atoms, 494 bonds, 21 residues, 1 model selected
> select add #5/H:544
481 atoms, 519 bonds, 22 residues, 1 model selected
> select add #5/H:545
501 atoms, 540 bonds, 23 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> combine #5 #10
Remapping chain ID 'A' in fold_r_e_model_0.cif #10 to 'J'
> hide #!5 models
> hide #!10 models
> hide #!6 models
> show #!6 models
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-combine-new-10.pdb models
> #6 relModel #6
> close #5-6
> close #3
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-combine-
> new-10_real_space_refined_009-coot-0.pdb
Chain information for R-combine-new-10_real_space_refined_009-coot-0.pdb #3
---
Chain | Description
A | 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
> select #3/I:263@C1'
1 atom, 1 residue, 1 model selected
> select up
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
568 atoms, 638 bonds, 26 residues, 1 model selected
> select up
12029 atoms, 13466 bonds, 562 residues, 1 model selected
> style sel stick
Changed 12029 atom styles
> cartoon sel
> view matrix models #3,1,0,0,-1.9467,0,1,0,-0.10847,0,0,1,7.3482
> show #!2 models
> view matrix models #3,1,0,0,-7.1235,0,1,0,7.0208,0,0,1,10.867
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.081361,0.9558,0.28254,-51.333,-0.18653,0.29308,-0.93772,377.82,-0.97907,0.023592,0.20213,383.28
> view matrix models
> #3,-0.73587,0.67047,0.094661,212.67,-0.014296,0.12438,-0.99213,384.48,-0.67697,-0.73143,-0.081946,520.04
> view matrix models
> #3,-0.67828,0.73014,-0.082663,227.73,-0.48269,-0.52755,-0.69908,539.31,-0.55403,-0.43427,0.71025,269.5
> view matrix models
> #3,-0.75581,0.48908,-0.43538,364.17,0.29428,-0.34026,-0.8931,383.9,-0.58494,-0.80314,0.11325,472.23
> view matrix models
> #3,-0.62216,0.69141,-0.36725,284.28,0.13733,-0.36544,-0.92065,427.31,-0.77075,-0.62323,0.13241,473.85
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.62216,0.69141,-0.36725,279.48,0.13733,-0.36544,-0.92065,440.75,-0.77075,-0.62323,0.13241,471.19
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.62945,0.76473,0.13777,158.96,-0.56326,-0.3269,-0.75887,545.5,-0.5353,-0.55527,0.6365,301.06
> view matrix models
> #3,-0.64716,0.74184,0.17566,158.74,-0.6528,-0.42024,-0.63028,553.8,-0.39375,-0.52256,0.75623,239.68
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.64716,0.74184,0.17566,180.45,-0.6528,-0.42024,-0.63028,550.95,-0.39375,-0.52256,0.75623,267.47
> view matrix models
> #3,-0.64716,0.74184,0.17566,194.29,-0.6528,-0.42024,-0.63028,575.74,-0.39375,-0.52256,0.75623,267.38
> fitmap #3 inMap #2
Fit molecule R-combine-new-10_real_space_refined_009-coot-0.pdb (#3) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 12029 atoms
average map value = 4.84, steps = 336
shifted from previous position = 22.5
rotated from previous position = 34.3 degrees
atoms outside contour = 4982, contour level = 3.0813
Position of R-combine-new-10_real_space_refined_009-coot-0.pdb (#3) relative
to cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
0.99999990 -0.00035549 -0.00029112 0.10616282
0.00035558 0.99999990 0.00029033 -0.11892637
0.00029102 -0.00029043 0.99999992 0.00255272
Axis -0.53422494 -0.53550080 0.65409678
Axis point 321.53908086 311.52305706 0.00000000
Rotation angle (degrees) 0.03114330
Shift along axis 0.00864007
> select #3/H:523
22 atoms, 24 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> show #14 models
> hide #!3 models
> ui tool show "Show Sequence Viewer"
> sequence chain #7/A #10/A #11/A #12/A #13/A #14/A #17/B #19/B #15/B
Alignment identifier is 1
> select #7/A #10/A #11/A #12/A #13/A #14/A #17/B #19/B #15/B
75538 atoms, 84634 bonds, 1 pseudobond, 3530 residues, 10 models selected
> select clear
> select #11/A:517 #12/A:517 #13/A:517 #14/A:517 #17/B:517 #15/B:517
120 atoms, 126 bonds, 6 residues, 6 models selected
> select #11/A:517 #12/A:517 #13/A:517 #14/A:517 #17/B:517 #15/B:517
120 atoms, 126 bonds, 6 residues, 6 models selected
. [ID: 1] region 9 chains [517] RMSD: 49.750
> select #11/A:517 #12/A:517 #13/A:517 #14/A:517 #17/B:517 #15/B:517
120 atoms, 126 bonds, 6 residues, 6 models selected
> select #11/A:517-524 #12/A:517-524 #13/A:517-524 #14/A:517-524 #17/B:517-524
> #15/B:517-524
1032 atoms, 1152 bonds, 48 residues, 6 models selected
. [ID: 1] region 9 chains [517-524] RMSD: 54.339
> ui tool show "Model Panel"
> show #13 models
> hide #14 models
> show #12 models
> hide #13 models
> show #11 models
> hide #12 models
> show #!10 models
> hide #11 models
> show #!7 models
> hide #!10 models
> show #15 models
> hide #!7 models
> show #17 models
> hide #15 models
> show #19 models
> hide #17 models
> hide #19 models
> show #13 models
> show #12 models
> hide #13 models
> show #13 models
> hide #12 models
> hide #13 models
> show #12 models
> show #11 models
> hide #12 models
> hide #11 models
> show #12 models
> select ~sel & ##selected
73040 atoms, 81840 bonds, 3416 residues, 6 models selected
> delete atoms (#12 & sel)
> delete bonds (#12 & sel)
> show #!2 models
Drag select of 8 residues, 16 shapes
> view matrix models #12,1,0,0,339.47,0,1,0,198.19,0,0,1,142.91
> view matrix models #12,1,0,0,329.64,0,1,0,171.65,0,0,1,274.23
> view matrix models #12,1,0,0,268.48,0,1,0,191.4,0,0,1,273.63
> view matrix models #12,1,0,0,254.32,0,1,0,205.99,0,0,1,243.25
> view matrix models #12,1,0,0,256.09,0,1,0,194.19,0,0,1,241.93
> show #!4 models
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.86506,0.26015,0.42894,264.38,-0.49886,0.53646,0.6807,201.64,-0.053031,-0.80283,0.59385,230.13
> view matrix models
> #12,0.0027527,0.33023,-0.9439,227.29,-0.42437,0.85508,0.29791,195.64,0.90549,0.39974,0.14249,234.92
> view matrix models
> #12,-0.398,0.041459,-0.91645,222.74,-0.54804,0.79039,0.27376,193.64,0.7357,0.6112,-0.29185,224.91
> view matrix models
> #12,-0.40336,0.24788,-0.88083,224.12,-0.766,0.43509,0.47322,194.37,0.50054,0.86559,0.014381,229.74
> view matrix models
> #12,0.18785,-0.07416,-0.97939,226.98,0.27242,-0.95409,0.1245,193.03,-0.94366,-0.2902,-0.15903,207.05
> view matrix models
> #12,0.91579,0.40036,-0.032223,256.01,0.38936,-0.90459,-0.17354,188.25,-0.098629,0.14638,-0.9843,200.24
> view matrix models
> #12,0.59239,0.6807,-0.43095,245.39,0.2705,-0.67191,-0.68947,177.14,-0.75888,0.29187,-0.58216,202.31
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.59239,0.6807,-0.43095,259.12,0.2705,-0.67191,-0.68947,171.34,-0.75888,0.29187,-0.58216,203.74
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.52605,0.67282,-0.52018,256.56,0.27622,-0.71365,-0.64374,172.21,-0.80435,0.19495,-0.56126,203.38
> view matrix models
> #12,0.55762,0.79184,-0.24911,262.92,-0.10892,-0.22771,-0.96762,163.26,-0.82292,0.5667,-0.040724,215.14
> view matrix models
> #12,0.57908,0.68475,-0.44247,258.76,-0.26099,-0.35847,-0.89632,162.77,-0.77236,0.63452,-0.028872,216.12
> view matrix models
> #12,0.91978,0.37523,-0.11495,267.85,0.15025,-0.60731,-0.78013,168.43,-0.36254,0.70027,-0.61497,208.37
> view matrix models
> #12,0.7033,0.30754,-0.64093,254.53,0.039845,-0.91722,-0.39639,174.13,-0.70978,0.25324,-0.65733,202.52
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.7033,0.30754,-0.64093,246.15,0.039845,-0.91722,-0.39639,178.71,-0.70978,0.25324,-0.65733,202.5
> view matrix models
> #12,0.7033,0.30754,-0.64093,247.58,0.039845,-0.91722,-0.39639,178.98,-0.70978,0.25324,-0.65733,203.64
> view matrix models
> #12,0.7033,0.30754,-0.64093,247.78,0.039845,-0.91722,-0.39639,179.33,-0.70978,0.25324,-0.65733,204.16
> view matrix models
> #12,0.7033,0.30754,-0.64093,248.24,0.039845,-0.91722,-0.39639,178.03,-0.70978,0.25324,-0.65733,205.27
> view matrix models
> #12,0.7033,0.30754,-0.64093,249.49,0.039845,-0.91722,-0.39639,177.7,-0.70978,0.25324,-0.65733,205.5
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.99507,-0.044604,0.088571,266.23,0.068404,-0.33793,-0.93868,168.85,0.0718,0.94011,-0.33321,222.53
> view matrix models
> #12,0.51867,-0.69356,0.49995,267.56,0.60863,-0.11117,-0.78563,178.35,0.60046,0.71177,0.36446,241.55
> view matrix models
> #12,0.045011,-0.94431,0.32595,258.18,0.93712,-0.073128,-0.34127,191.03,0.3461,0.32082,0.88164,248.18
> view matrix models
> #12,-0.062893,-0.97457,0.21507,254.66,0.93873,-0.13094,-0.3188,191.31,0.33885,0.18185,0.9231,248.48
> view matrix models
> #12,-0.157,-0.98214,0.10366,251.36,0.94634,-0.17963,-0.26864,192.27,0.28247,0.055921,0.95765,248.19
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.157,-0.98214,0.10366,246.18,0.94634,-0.17963,-0.26864,190.76,0.28247,0.055921,0.95765,249.79
> view matrix models
> #12,-0.157,-0.98214,0.10366,246.85,0.94634,-0.17963,-0.26864,190.62,0.28247,0.055921,0.95765,249.75
> view matrix models
> #12,-0.157,-0.98214,0.10366,245.63,0.94634,-0.17963,-0.26864,191.77,0.28247,0.055921,0.95765,249.16
> fitmap #12 inMap #2
Fit molecule fold_r_e_model_2.cif (#12) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 172 atoms
average map value = 4.951, steps = 120
shifted from previous position = 2.01
rotated from previous position = 18.8 degrees
atoms outside contour = 67, contour level = 3.0813
Position of fold_r_e_model_2.cif (#12) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
-0.86672413 0.28289916 -0.41080088 204.15446232
-0.22996757 -0.95748442 -0.17417952 217.12360180
-0.44261068 -0.05649472 0.89493248 240.98896718
Axis 0.22324458 0.06034225 -0.97289294
Axis point 145.42838977 99.25322946 0.00000000
Rotation angle (degrees) 164.71751412
Shift along axis -175.77836152
> select #4/H:523
23 atoms, 25 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #12/A:524
22 atoms, 24 bonds, 1 residue, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.064363,-0.99733,-0.034579,244.95,0.97788,-0.056123,-0.20147,192.97,0.19899,-0.046781,0.97888,249.53
> view matrix models
> #12,0.20028,-0.88782,0.41432,257.37,0.86686,-0.03648,-0.49721,185.76,0.45655,0.45874,0.76231,249.42
> view matrix models
> #12,0.37851,-0.89878,0.22119,255.14,0.79828,0.19604,-0.56949,184.41,0.46848,0.39213,0.79168,249.9
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.37851,-0.89878,0.22119,254.73,0.79828,0.19604,-0.56949,184.69,0.46848,0.39213,0.79168,249.4
> view matrix models
> #12,0.37851,-0.89878,0.22119,254.97,0.79828,0.19604,-0.56949,184.12,0.46848,0.39213,0.79168,249.39
> select #4/H:522
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #4/H:521
40 atoms, 42 bonds, 2 residues, 1 model selected
> select add #4/H:520
63 atoms, 67 bonds, 3 residues, 1 model selected
> select add #4/H:519
83 atoms, 88 bonds, 4 residues, 1 model selected
> select add #4/H:518
106 atoms, 113 bonds, 5 residues, 1 model selected
> select add #4/H:517
126 atoms, 134 bonds, 6 residues, 1 model selected
> select add #4/H:516
148 atoms, 158 bonds, 7 residues, 1 model selected
> select add #4/H:514
168 atoms, 179 bonds, 8 residues, 1 model selected
> select add #4/H:513
190 atoms, 203 bonds, 9 residues, 1 model selected
> select add #4/H:515
213 atoms, 228 bonds, 10 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> select add #12/A:524
22 atoms, 24 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!3 models
> hide #!4 models
> close #4
> select #3/H:518
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #3/H:517
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add #3/H:516
65 atoms, 70 bonds, 3 residues, 1 model selected
> select add #3/H:515
88 atoms, 95 bonds, 4 residues, 1 model selected
> select add #3/H:514
108 atoms, 116 bonds, 5 residues, 1 model selected
> select add #3/H:513
130 atoms, 140 bonds, 6 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #3/E:419
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #3/E:418
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add #3/E:417
64 atoms, 69 bonds, 3 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> combine #3 #12
Remapping chain ID 'A' in fold_r_e_model_2.cif #12 to 'B'
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-combine-new-11.pdb models
> #4 relModel #4
> hide #12 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> show #13 models
> select #7/A #10/A #11/A #12/A #13/A #14/A #17/B #19/B #15/B
63343 atoms, 70969 bonds, 1 pseudobond, 2960 residues, 10 models selected
> select clear
> select #7/A:194 #11/A:194 #13/A:194 #14/A:194 #17/B:194 #15/B:194
132 atoms, 144 bonds, 6 residues, 6 models selected
> select #7/A:194-195 #11/A:194-195 #13/A:194-195 #14/A:194-195 #17/B:194-195
> #15/B:194-195
264 atoms, 294 bonds, 12 residues, 6 models selected
. [ID: 1] region 9 chains [194-195] RMSD: 231.610
> select #7/A:195 #11/A:195 #13/A:195 #14/A:195 #17/B:195 #15/B:195
132 atoms, 144 bonds, 6 residues, 6 models selected
> select #7/A:195-198 #11/A:195-216 #13/A:195-216 #14/A:195-216 #17/B:195-216
> #15/B:195-216
2468 atoms, 2763 bonds, 114 residues, 6 models selected
. [ID: 1] region 9 chains [195-216] RMSD: 133.343
> select #7/A:195 #11/A:195 #13/A:195 #14/A:195 #17/B:195 #15/B:195
132 atoms, 144 bonds, 6 residues, 6 models selected
> select #7/A:195-198 #11/A:195-218 #13/A:195-218 #14/A:195-218 #17/B:195-218
> #15/B:195-218
2678 atoms, 2998 bonds, 124 residues, 6 models selected
. [ID: 1] region 9 chains [195-218] RMSD: 131.279
> show #11 models
> hide #13 models
> show #12 models
> hide #11 models
> show #13 models
> hide #12 models
> show #14 models
> hide #13 models
> show #15 models
> hide #14 models
> select add #15/B:219
2700 atoms, 3022 bonds, 125 residues, 6 models selected
> select add #15/B:220
2722 atoms, 3046 bonds, 126 residues, 6 models selected
> select add #15/B:221
2742 atoms, 3067 bonds, 127 residues, 6 models selected
> select add #15/B:222
2764 atoms, 3091 bonds, 128 residues, 6 models selected
> select add #15/B:223
2787 atoms, 3116 bonds, 129 residues, 6 models selected
> select add #15/B:224
2809 atoms, 3140 bonds, 130 residues, 6 models selected
> select add #15/B:225
2829 atoms, 3161 bonds, 131 residues, 6 models selected
> select add #15/B:226
2852 atoms, 3186 bonds, 132 residues, 6 models selected
> select add #15/B:227
2872 atoms, 3207 bonds, 133 residues, 6 models selected
> select add #15/B:228
2892 atoms, 3228 bonds, 134 residues, 6 models selected
> select add #15/B:229
2912 atoms, 3249 bonds, 135 residues, 6 models selected
> select add #15/B:230
2932 atoms, 3270 bonds, 136 residues, 6 models selected
> select add #15/B:231
2952 atoms, 3291 bonds, 137 residues, 6 models selected
> select add #15/B:232
2975 atoms, 3316 bonds, 138 residues, 6 models selected
> select add #15/B:233
2995 atoms, 3337 bonds, 139 residues, 6 models selected
> select add #15/B:234
3018 atoms, 3362 bonds, 140 residues, 6 models selected
> select add #15/B:235
3041 atoms, 3387 bonds, 141 residues, 6 models selected
> select add #15/B:236
3063 atoms, 3411 bonds, 142 residues, 6 models selected
> select add #15/B:237
3085 atoms, 3435 bonds, 143 residues, 6 models selected
> select add #15/B:238
3107 atoms, 3459 bonds, 144 residues, 6 models selected
> select add #15/B:239
3129 atoms, 3483 bonds, 145 residues, 6 models selected
> select add #15/B:240
3152 atoms, 3508 bonds, 146 residues, 6 models selected
> select add #15/B:241
3174 atoms, 3532 bonds, 147 residues, 6 models selected
> select add #15/B:242
3196 atoms, 3556 bonds, 148 residues, 6 models selected
> select add #15/B:244
3216 atoms, 3577 bonds, 149 residues, 6 models selected
> select add #15/B:243
3236 atoms, 3598 bonds, 150 residues, 6 models selected
> select ~sel & ##selected
59467 atoms, 66629 bonds, 1 pseudobond, 2782 residues, 7 models selected
> delete atoms (#15 & sel)
> delete bonds (#15 & sel)
> show #!2 models
Drag select of 50 residues, 100 shapes
> view matrix models #15,1,0,0,143.27,0,1,0,276.32,0,0,1,283.04
> view matrix models #15,1,0,0,228.97,0,1,0,242.35,0,0,1,283.29
> ui mousemode right "rotate selected models"
> view matrix models
> #15,-0.93122,-0.35754,-0.070627,276.27,-0.24588,0.75939,-0.60238,227.29,0.26901,-0.54358,-0.79508,212.65
> view matrix models
> #15,-0.8632,-0.50333,-0.039196,274.02,-0.41206,0.65755,0.63074,270.68,-0.2917,0.56061,-0.775,239.31
> view matrix models
> #15,-0.69915,-0.70728,-0.10464,265.44,-0.1885,0.04116,0.98121,269.93,-0.68968,0.70574,-0.1621,271.41
> view matrix models
> #15,-0.7751,-0.62917,0.057911,273.52,0.0026634,0.088401,0.99608,265.62,-0.63183,0.77222,-0.066844,273.54
> ui mousemode right "translate selected models"
> view matrix models
> #15,-0.7751,-0.62917,0.057911,222.55,0.0026634,0.088401,0.99608,242.18,-0.63183,0.77222,-0.066844,286.13
> view matrix models
> #15,-0.7751,-0.62917,0.057911,226.14,0.0026634,0.088401,0.99608,242.21,-0.63183,0.77222,-0.066844,257.12
> view matrix models
> #15,-0.7751,-0.62917,0.057911,226.37,0.0026634,0.088401,0.99608,230.52,-0.63183,0.77222,-0.066844,265.63
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> close #3-4
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-combine-new-11-coot-0.pdb
Chain information for R-combine-new-11-coot-0.pdb #3
---
Chain | Description
A | No description available
D | No description available
F | No description available
G | No description available
H | No description available
I | No description available
> select #3/H:75@C5'
1 atom, 1 residue, 1 model selected
> select up
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
9284 atoms, 10394 bonds, 434 residues, 1 model selected
> select up
11963 atoms, 13394 bonds, 559 residues, 1 model selected
> select up
64677 atoms, 72451 bonds, 3023 residues, 16 models selected
> select up
64677 atoms, 72451 bonds, 3023 residues, 16 models selected
> select up
64677 atoms, 72451 bonds, 3023 residues, 16 models selected
> select up
64677 atoms, 72451 bonds, 3023 residues, 16 models selected
> select up
64677 atoms, 72451 bonds, 3023 residues, 16 models selected
> select up
64677 atoms, 72451 bonds, 3023 residues, 16 models selected
> select up
64677 atoms, 72451 bonds, 3023 residues, 16 models selected
> select up
64677 atoms, 72451 bonds, 3023 residues, 16 models selected
> select down
11963 atoms, 13394 bonds, 559 residues, 1 model selected
> style sel stick
Changed 11963 atom styles
> cartoon sel
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.051379,0.72417,0.6877,-82.422,-0.34872,0.65828,-0.66714,279.3,-0.93582,-0.20554,0.28635,387.15
> view matrix models
> #3,-0.018181,0.99871,-0.047468,39.711,-0.54105,-0.049752,-0.83952,486.97,-0.84079,0.01042,0.54126,272.74
> view matrix models
> #3,0.078824,0.99587,-0.045109,19.428,-0.55158,0.0058763,-0.8341,477.8,-0.83039,0.090628,0.54977,254.01
> fitmap #3 inMap #2
Fit molecule R-combine-new-11-coot-0.pdb (#3) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 11963 atoms
average map value = 4.789, steps = 324
shifted from previous position = 28.7
rotated from previous position = 19 degrees
atoms outside contour = 4999, contour level = 3.0813
Position of R-combine-new-11-coot-0.pdb (#3) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
0.99999999 -0.00010067 -0.00003356 0.03298488
0.00010067 0.99999999 -0.00005365 -0.00938195
0.00003357 0.00005365 1.00000000 -0.03614252
Axis 0.45119018 -0.28227184 0.84661091
Axis point 129.85978764 386.20271697 0.00000000
Rotation angle (degrees) 0.00681316
Shift along axis -0.01306793
> select clear
> select #15/B:243
20 atoms, 21 bonds, 1 residue, 1 model selected
> view matrix models
> #15,-0.9062,0.076465,0.41589,248.31,0.41477,0.35215,0.83902,216.7,-0.082299,0.93282,-0.35083,242.91
> view matrix models
> #15,-0.93655,-0.24639,0.24933,240.66,-0.095336,0.86351,0.49523,224.48,-0.33733,0.44004,-0.83221,229.6
> view matrix models
> #15,-0.96951,0.021282,0.24412,243.97,0.14853,0.8434,0.51635,218.29,-0.1949,0.53686,-0.82085,227
> ui mousemode right "translate selected models"
> view matrix models
> #15,-0.96951,0.021282,0.24412,232.19,0.14853,0.8434,0.51635,230.07,-0.1949,0.53686,-0.82085,225.32
> ui mousemode right "rotate selected models"
> view matrix models
> #15,-0.15362,-0.64857,0.7455,219.54,0.61846,0.5253,0.58444,216.32,-0.77065,0.55084,0.32042,278.08
> view matrix models
> #15,-0.36921,-0.45703,0.8092,229.35,0.6655,0.47774,0.57347,214.22,-0.64868,0.75026,0.12777,270.43
> ui mousemode right "translate selected models"
> view matrix models
> #15,-0.36921,-0.45703,0.8092,237,0.6655,0.47774,0.57347,220.72,-0.64868,0.75026,0.12777,268.92
> view matrix models
> #15,-0.36921,-0.45703,0.8092,236.75,0.6655,0.47774,0.57347,228.23,-0.64868,0.75026,0.12777,267.7
> view matrix models
> #15,-0.36921,-0.45703,0.8092,235.99,0.6655,0.47774,0.57347,225.78,-0.64868,0.75026,0.12777,267.61
> view matrix models
> #15,-0.36921,-0.45703,0.8092,236.33,0.6655,0.47774,0.57347,228.07,-0.64868,0.75026,0.12777,266.61
> view matrix models
> #15,-0.36921,-0.45703,0.8092,235.99,0.6655,0.47774,0.57347,227.02,-0.64868,0.75026,0.12777,266.63
> view matrix models
> #15,-0.36921,-0.45703,0.8092,237.05,0.6655,0.47774,0.57347,226.66,-0.64868,0.75026,0.12777,266.32
> fitmap #15 inMap #2
Fit molecule fold_r_e_m_model_0.cif (#15) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 1076 atoms
average map value = 4.02, steps = 248
shifted from previous position = 10
rotated from previous position = 39.5 degrees
atoms outside contour = 502, contour level = 3.0813
Position of fold_r_e_m_model_0.cif (#15) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
0.59862331 -0.80049940 -0.02916953 185.40712798
-0.49221379 -0.39632454 0.77501771 219.34411492
-0.63196181 -0.44958602 -0.63126594 195.82380617
Axis -0.87515177 0.43077994 0.22031347
Axis point 0.00000000 202.22531386 67.63578282
Rotation angle (degrees) 135.60089312
Shift along axis -24.62770874
> view matrix models
> #15,-0.6372,-0.19851,0.74469,241.76,0.26478,0.85106,0.45342,241.07,-0.72379,0.4861,-0.48974,242.22
> view matrix models
> #15,-0.6372,-0.19851,0.74469,245.02,0.26478,0.85106,0.45342,241.58,-0.72379,0.4861,-0.48974,241.58
> ui mousemode right "rotate selected models"
> view matrix models
> #15,-0.62418,-0.22136,0.74927,244.59,0.26418,0.84273,0.46905,242.02,-0.73526,0.49071,-0.46753,242.65
> view matrix models
> #15,-0.53771,-0.35056,0.7668,241.55,0.27792,0.78494,0.55374,243.82,-0.79601,0.51086,-0.32464,249.13
> hide #!3 models
> select clear
Drag select of 24 residues, 48 shapes
> delete atoms sel
> delete bonds sel
Drag select of 2 residues, 4 shapes
> delete atoms sel
> delete bonds sel
> show #!2 models
> fitmap #15 inMap #2
Fit molecule fold_r_e_m_model_0.cif (#15) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 518 atoms
average map value = 3.975, steps = 168
shifted from previous position = 6.13
rotated from previous position = 9.54 degrees
atoms outside contour = 226, contour level = 3.0813
Position of fold_r_e_m_model_0.cif (#15) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
0.58162625 -0.80314204 -0.12912695 179.85967399
-0.52902395 -0.49404402 0.68996679 210.41378925
-0.61793573 -0.33299155 -0.71223034 193.74489505
Axis -0.87701237 0.41907019 0.23500953
Axis point 0.00000000 184.76005643 80.51979040
Rotation angle (degrees) 144.32362317
Shift along axis -24.02911449
> ui mousemode right "translate selected models"
> select #15/B:208
20 atoms, 21 bonds, 1 residue, 1 model selected
> view matrix models
> #15,-0.66843,-0.29005,0.68489,237.34,0.26644,0.76634,0.58458,244.16,-0.69441,0.57323,-0.43496,245.35
> view matrix models
> #15,-0.66843,-0.29005,0.68489,236.19,0.26644,0.76634,0.58458,241.5,-0.69441,0.57323,-0.43496,247.27
> view matrix models
> #15,-0.66843,-0.29005,0.68489,237.51,0.26644,0.76634,0.58458,240.23,-0.69441,0.57323,-0.43496,246.99
> view matrix models
> #15,-0.66843,-0.29005,0.68489,235.7,0.26644,0.76634,0.58458,242.33,-0.69441,0.57323,-0.43496,246.52
> show #!3 models
> volume #2 level 9.732
> view matrix models
> #15,-0.66843,-0.29005,0.68489,235.81,0.26644,0.76634,0.58458,242.94,-0.69441,0.57323,-0.43496,246.7
> close #3
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-combine-new-11-coot-0.pdb
Chain information for R-combine-new-11-coot-0.pdb #3
---
Chain | Description
A | No description available
D | No description available
F | No description available
G | No description available
H | No description available
I | No description available
> select #3/H:65@C5'
1 atom, 1 residue, 1 model selected
> select up
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
9306 atoms, 10419 bonds, 435 residues, 1 model selected
> select up
11985 atoms, 13419 bonds, 560 residues, 1 model selected
> style sel stick
Changed 11985 atom styles
> cartoon sel
> volume #2 level 4.005
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.28517,0.63069,0.72174,-121.71,-0.69902,0.65205,-0.2936,273.25,-0.65579,-0.42078,0.62681,294.73
> view matrix models
> #3,-0.63979,0.71414,-0.28402,271.95,-0.61089,-0.69679,-0.37589,521.32,-0.46634,-0.066985,0.88207,135.03
> view matrix models
> #3,-0.3072,0.95159,-0.010074,99.826,-0.4499,-0.15455,-0.87961,495.7,-0.83858,-0.26568,0.4756,336.71
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.3072,0.95159,-0.010074,137.36,-0.4499,-0.15455,-0.87961,506.29,-0.83858,-0.26568,0.4756,353.27
> view matrix models
> #3,-0.3072,0.95159,-0.010074,132.93,-0.4499,-0.15455,-0.87961,519.12,-0.83858,-0.26568,0.4756,360.7
> view matrix models
> #3,-0.3072,0.95159,-0.010074,111.09,-0.4499,-0.15455,-0.87961,530.74,-0.83858,-0.26568,0.4756,375.41
> fitmap #3 inMap #2
Fit molecule R-combine-new-11-coot-0.pdb (#3) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 11985 atoms
average map value = 4.998, steps = 172
shifted from previous position = 19.5
rotated from previous position = 6.38 degrees
atoms outside contour = 5324, contour level = 4.005
Position of R-combine-new-11-coot-0.pdb (#3) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
0.99999999 -0.00003225 -0.00016822 0.03533317
0.00003228 0.99999999 0.00014937 -0.02226528
0.00016822 -0.00014938 0.99999998 -0.01210345
Axis -0.65725665 -0.74017593 0.14196226
Axis point 64.83711940 0.00000000 176.97440828
Rotation angle (degrees) 0.01302169
Shift along axis -0.00846097
> select clear
> volume #2 level 9.239
> show #13 models
> hide #!15 models
> hide #!3 models
> hide #!2 models
> select #13/A:194
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #13/A:193
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add #13/A:526
65 atoms, 70 bonds, 3 residues, 1 model selected
> select add #13/A:525
85 atoms, 91 bonds, 4 residues, 1 model selected
> select add #13/A:524
107 atoms, 115 bonds, 5 residues, 1 model selected
> select add #13/A:523
129 atoms, 139 bonds, 6 residues, 1 model selected
> select add #13/A:522
152 atoms, 164 bonds, 7 residues, 1 model selected
> select add #13/A:350
174 atoms, 188 bonds, 8 residues, 1 model selected
> select subtract #13/A:350
152 atoms, 164 bonds, 7 residues, 1 model selected
> select add #13/A:521
172 atoms, 185 bonds, 8 residues, 1 model selected
> select add #13/A:519
194 atoms, 209 bonds, 9 residues, 1 model selected
> select add #13/A:520
214 atoms, 230 bonds, 10 residues, 1 model selected
> select add #13/A:199
236 atoms, 254 bonds, 11 residues, 1 model selected
> select add #13/A:198
256 atoms, 275 bonds, 12 residues, 1 model selected
> select add #13/A:197
279 atoms, 300 bonds, 13 residues, 1 model selected
> select add #13/A:196
302 atoms, 325 bonds, 14 residues, 1 model selected
> select add #13/A:195
324 atoms, 349 bonds, 15 residues, 1 model selected
> select add #13/A:346
344 atoms, 370 bonds, 16 residues, 1 model selected
> select add #13/A:345
367 atoms, 395 bonds, 17 residues, 1 model selected
> select add #13/A:344
390 atoms, 420 bonds, 18 residues, 1 model selected
> select add #13/A:343
410 atoms, 441 bonds, 19 residues, 1 model selected
> select add #13/A:342
430 atoms, 462 bonds, 20 residues, 1 model selected
> select add #13/A:200
450 atoms, 483 bonds, 21 residues, 1 model selected
> select add #13/A:201
472 atoms, 507 bonds, 22 residues, 1 model selected
> select add #13/A:341
492 atoms, 528 bonds, 23 residues, 1 model selected
> select add #13/A:340
512 atoms, 549 bonds, 24 residues, 1 model selected
> select add #13/A:339
534 atoms, 573 bonds, 25 residues, 1 model selected
> select add #13/A:202
556 atoms, 597 bonds, 26 residues, 1 model selected
> select add #13/A:203
579 atoms, 622 bonds, 27 residues, 1 model selected
> select add #13/A:204
601 atoms, 646 bonds, 28 residues, 1 model selected
> select add #13/A:205
621 atoms, 667 bonds, 29 residues, 1 model selected
> select add #13/A:206
641 atoms, 688 bonds, 30 residues, 1 model selected
> select add #13/A:338
664 atoms, 713 bonds, 31 residues, 1 model selected
> select add #13/A:337
686 atoms, 737 bonds, 32 residues, 1 model selected
> select add #13/A:336
709 atoms, 762 bonds, 33 residues, 1 model selected
> select add #13/A:335
731 atoms, 786 bonds, 34 residues, 1 model selected
> select add #13/A:334
753 atoms, 810 bonds, 35 residues, 1 model selected
> select add #13/A:207
773 atoms, 831 bonds, 36 residues, 1 model selected
> select add #13/A:208
793 atoms, 852 bonds, 37 residues, 1 model selected
> select add #13/A:209
813 atoms, 873 bonds, 38 residues, 1 model selected
> select add #13/A:210
836 atoms, 898 bonds, 39 residues, 1 model selected
> select add #13/A:333
856 atoms, 919 bonds, 40 residues, 1 model selected
> select add #13/A:211
879 atoms, 944 bonds, 41 residues, 1 model selected
> select add #13/A:212
902 atoms, 969 bonds, 42 residues, 1 model selected
> select add #13/A:213
925 atoms, 994 bonds, 43 residues, 1 model selected
> select add #13/A:214
948 atoms, 1019 bonds, 44 residues, 1 model selected
> select add #13/A:300
968 atoms, 1040 bonds, 45 residues, 1 model selected
> select add #13/A:299
988 atoms, 1061 bonds, 46 residues, 1 model selected
> select add #13/A:298
1008 atoms, 1082 bonds, 47 residues, 1 model selected
> select add #13/A:297
1028 atoms, 1103 bonds, 48 residues, 1 model selected
> select add #13/A:296
1050 atoms, 1127 bonds, 49 residues, 1 model selected
> select add #13/A:295
1073 atoms, 1152 bonds, 50 residues, 1 model selected
> select add #13/A:294
1095 atoms, 1176 bonds, 51 residues, 1 model selected
> select add #13/A:293
1117 atoms, 1200 bonds, 52 residues, 1 model selected
> select add #13/A:216
1137 atoms, 1221 bonds, 53 residues, 1 model selected
> select add #13/A:215
1159 atoms, 1245 bonds, 54 residues, 1 model selected
> select add #13/A:217
1181 atoms, 1269 bonds, 55 residues, 1 model selected
> select add #13/A:218
1201 atoms, 1290 bonds, 56 residues, 1 model selected
> select add #13/A:219
1223 atoms, 1314 bonds, 57 residues, 1 model selected
> select add #13/A:292
1245 atoms, 1338 bonds, 58 residues, 1 model selected
> select add #13/A:291
1267 atoms, 1362 bonds, 59 residues, 1 model selected
> select add #13/A:290
1287 atoms, 1383 bonds, 60 residues, 1 model selected
> select add #13/A:301
1307 atoms, 1404 bonds, 61 residues, 1 model selected
> select add #13/A:302
1327 atoms, 1425 bonds, 62 residues, 1 model selected
> select add #13/A:303
1347 atoms, 1446 bonds, 63 residues, 1 model selected
> select add #13/A:304
1367 atoms, 1467 bonds, 64 residues, 1 model selected
> select add #13/A:305
1390 atoms, 1492 bonds, 65 residues, 1 model selected
> select add #13/A:306
1412 atoms, 1516 bonds, 66 residues, 1 model selected
> select add #13/A:307
1432 atoms, 1537 bonds, 67 residues, 1 model selected
> select add #13/A:332
1454 atoms, 1561 bonds, 68 residues, 1 model selected
> select add #13/A:331
1476 atoms, 1585 bonds, 69 residues, 1 model selected
> select add #13/A:330
1496 atoms, 1606 bonds, 70 residues, 1 model selected
> select add #13/A:329
1516 atoms, 1627 bonds, 71 residues, 1 model selected
> select add #13/A:328
1536 atoms, 1648 bonds, 72 residues, 1 model selected
> select add #13/A:327
1559 atoms, 1673 bonds, 73 residues, 1 model selected
> select add #13/A:326
1582 atoms, 1698 bonds, 74 residues, 1 model selected
> select add #13/A:325
1605 atoms, 1723 bonds, 75 residues, 1 model selected
> select add #13/A:324
1625 atoms, 1744 bonds, 76 residues, 1 model selected
> select add #13/A:323
1647 atoms, 1768 bonds, 77 residues, 1 model selected
> select add #13/A:322
1667 atoms, 1789 bonds, 78 residues, 1 model selected
> select add #13/A:321
1689 atoms, 1813 bonds, 79 residues, 1 model selected
> select add #13/A:320
1711 atoms, 1837 bonds, 80 residues, 1 model selected
> select add #13/A:319
1733 atoms, 1861 bonds, 81 residues, 1 model selected
> select add #13/A:318
1756 atoms, 1886 bonds, 82 residues, 1 model selected
> select add #13/A:317
1778 atoms, 1910 bonds, 83 residues, 1 model selected
> select add #13/A:316
1798 atoms, 1931 bonds, 84 residues, 1 model selected
> select add #13/A:315
1820 atoms, 1955 bonds, 85 residues, 1 model selected
> select add #13/A:314
1840 atoms, 1976 bonds, 86 residues, 1 model selected
> select add #13/A:313
1860 atoms, 1997 bonds, 87 residues, 1 model selected
> select add #13/A:312
1882 atoms, 2021 bonds, 88 residues, 1 model selected
> select add #13/A:311
1904 atoms, 2045 bonds, 89 residues, 1 model selected
> select add #13/A:310
1927 atoms, 2070 bonds, 90 residues, 1 model selected
> select add #13/A:309
1949 atoms, 2094 bonds, 91 residues, 1 model selected
> select add #13/A:308
1972 atoms, 2119 bonds, 92 residues, 1 model selected
> select ~sel & ##selected
10373 atoms, 11624 bonds, 485 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!2 models
> show #!3 models
Drag select of 92 residues, 2 pseudobonds, 184 shapes
> select clear
Drag select of 92 residues, 2 pseudobonds, 184 shapes
> view matrix models #13,1,0,0,71.27,0,1,0,378.15,0,0,1,74.179
> view matrix models #13,1,0,0,229.58,0,1,0,452.18,0,0,1,209.56
> view matrix models #13,1,0,0,177.6,0,1,0,231.58,0,0,1,199.25
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.53068,0.2509,0.80958,170.51,-0.53517,0.83988,0.090517,233.79,-0.65724,-0.4813,0.57998,208.59
> view matrix models
> #13,0.43063,0.35563,0.82951,173.37,-0.34777,0.91351,-0.2111,239.4,-0.83284,-0.19757,0.51706,217.7
> view matrix models
> #13,-0.12806,0.96437,0.23151,206.51,0.6934,0.25396,-0.67432,222.82,-0.70908,0.074176,-0.70121,249.16
> view matrix models
> #13,-0.70681,0.40963,-0.57674,221.61,0.45142,-0.36654,-0.81356,217.33,-0.54465,-0.83538,0.074159,212.37
> view matrix models
> #13,-0.65088,0.63602,-0.41453,221.43,-0.28992,-0.71288,-0.63855,216.39,-0.70164,-0.29544,0.64839,211.67
> view matrix models
> #13,-0.11064,0.83784,-0.53458,220.46,0.23952,-0.49955,-0.83251,217.35,-0.96457,-0.22016,-0.14541,234.59
> view matrix models
> #13,0.22307,0.49324,-0.84081,216.09,0.95865,-0.26739,0.097475,190.87,-0.17674,-0.82778,-0.53249,220.9
> view matrix models
> #13,0.28919,0.60789,-0.73949,215.08,0.9022,0.085155,0.42282,190.94,0.32,-0.78944,-0.52381,214.71
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.28919,0.60789,-0.73949,217.45,0.9022,0.085155,0.42282,175.34,0.32,-0.78944,-0.52381,223.09
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.11525,0.53673,-0.83585,223.71,0.44779,-0.72303,-0.52603,187.48,-0.88668,-0.43491,-0.15702,237.84
> view matrix models
> #13,-0.40635,0.55921,-0.72261,225.64,-0.34614,-0.82611,-0.44467,194.77,-0.84562,0.069434,0.52926,231.29
> view matrix models
> #13,-0.4065,0.75592,-0.51316,224.74,-0.85933,-0.5071,-0.066278,199.41,-0.31033,0.41403,0.85573,223.52
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.4065,0.75592,-0.51316,236.42,-0.85933,-0.5071,-0.066278,199.21,-0.31033,0.41403,0.85573,218.33
> view matrix models
> #13,-0.4065,0.75592,-0.51316,241.71,-0.85933,-0.5071,-0.066278,209.27,-0.31033,0.41403,0.85573,228.78
> fitmap #13 inMap #2
Fit molecule fold_r_e_model_3.cif (#13) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 1972 atoms
average map value = 2.914, steps = 128
shifted from previous position = 3.58
rotated from previous position = 14.3 degrees
atoms outside contour = 1820, contour level = 9.2394
Position of fold_r_e_model_3.cif (#13) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
0.69678775 -0.18347612 -0.69341427 213.02952633
-0.44626107 0.64595376 -0.61935030 215.79148867
0.56154954 0.74099950 0.36821442 211.19975463
Axis 0.72770521 -0.67133005 -0.14057412
Axis point 0.00000000 -1.54843213 328.12780390
Rotation angle (degrees) 69.17725945
Shift along axis -19.53383584
> view matrix models
> #13,-0.59057,0.68723,-0.42302,240.98,-0.79117,-0.59634,0.13575,205.92,-0.15898,0.41485,0.89589,226.95
> view matrix models
> #13,-0.59057,0.68723,-0.42302,245.13,-0.79117,-0.59634,0.13575,204.34,-0.15898,0.41485,0.89589,221.57
> view matrix models
> #13,-0.59057,0.68723,-0.42302,249.4,-0.79117,-0.59634,0.13575,206.01,-0.15898,0.41485,0.89589,218.92
> view matrix models
> #13,-0.59057,0.68723,-0.42302,249.41,-0.79117,-0.59634,0.13575,205.98,-0.15898,0.41485,0.89589,218.97
> view matrix models
> #13,-0.59057,0.68723,-0.42302,247.57,-0.79117,-0.59634,0.13575,204.96,-0.15898,0.41485,0.89589,223.81
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.34473,0.55016,-0.76058,249.36,-0.62285,-0.74025,-0.25315,208.8,-0.70229,0.38646,0.59786,237.11
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.34473,0.55016,-0.76058,250.03,-0.62285,-0.74025,-0.25315,209.89,-0.70229,0.38646,0.59786,236.15
> view matrix models
> #13,-0.34473,0.55016,-0.76058,250.38,-0.62285,-0.74025,-0.25315,210.51,-0.70229,0.38646,0.59786,235.62
> view matrix models
> #13,-0.34473,0.55016,-0.76058,250.22,-0.62285,-0.74025,-0.25315,211.24,-0.70229,0.38646,0.59786,235.12
> hide #!3 models
> select clear
> select #13/A:526
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #13/A:525
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add #13/A:524
65 atoms, 70 bonds, 3 residues, 1 model selected
> select add #13/A:523
87 atoms, 94 bonds, 4 residues, 1 model selected
> select add #13/A:522
110 atoms, 119 bonds, 5 residues, 1 model selected
> select add #13/A:520
150 atoms, 140 bonds, 7 residues, 1 model selected
> select add #13/A:519
172 atoms, 164 bonds, 8 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!2 models
> ui mousemode right "translate selected models"
> fitmap #13 inMap #2
Fit molecule fold_r_e_model_3.cif (#13) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 1800 atoms
average map value = 2.682, steps = 120
shifted from previous position = 1.67
rotated from previous position = 18.8 degrees
atoms outside contour = 1679, contour level = 9.2394
Position of fold_r_e_model_3.cif (#13) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
0.95202829 -0.01671453 -0.30555319 206.44337987
-0.28928621 0.27641526 -0.91646500 221.51639412
0.09977785 0.96089293 0.25831986 218.77734156
Axis 0.96777953 -0.20894848 -0.14051092
Axis point 0.00000000 -23.27751178 288.07572905
Rotation angle (degrees) 75.91378230
Shift along axis 122.76555778
> select add #13/A:194
22 atoms, 24 bonds, 1 residue, 1 model selected
> select subtract #13/A:194
Nothing selected
> select add #13/A:193
20 atoms, 21 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> fitmap #13 inMap #2
Fit molecule fold_r_e_model_3.cif (#13) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 1780 atoms
average map value = 2.684, steps = 40
shifted from previous position = 0.2
rotated from previous position = 0.353 degrees
atoms outside contour = 1658, contour level = 9.2394
Position of fold_r_e_model_3.cif (#13) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
0.95022872 -0.01523710 -0.31118035 206.65061815
-0.29497918 0.27743104 -0.91434091 221.37071479
0.10026299 0.96062472 0.25912831 218.74496789
Axis 0.96654938 -0.21210005 -0.14420773
Axis point 0.00000000 -23.29734571 288.64483855
Rotation angle (degrees) 75.91305403
Shift along axis 121.24057201
> select #13/A:345
23 atoms, 25 bonds, 1 residue, 1 model selected
> view matrix models
> #13,-0.51589,0.29366,-0.80475,248.47,-0.55888,-0.82733,0.05637,197.77,-0.64925,0.47884,0.59093,234.13
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.31452,0.088013,-0.94516,243.63,-0.44297,-0.89424,0.064135,194.31,-0.83956,0.43885,0.32025,241.76
> view matrix models
> #13,-0.30985,0.40243,-0.86142,249.77,-0.34383,-0.89212,-0.2931,200.92,-0.88644,0.20537,0.41479,234.33
> view matrix models
> #13,-0.77013,0.5129,-0.37925,247.98,-0.61395,-0.75733,0.22253,196.52,-0.17308,0.40422,0.89814,218.85
> view matrix models
> #13,-0.67804,-0.13835,-0.72189,238.14,-0.30462,-0.84092,0.44728,185.01,-0.66893,0.52317,0.52803,237.14
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.67804,-0.13835,-0.72189,245.18,-0.30462,-0.84092,0.44728,191.27,-0.66893,0.52317,0.52803,248.09
> view matrix models
> #13,-0.67804,-0.13835,-0.72189,249.59,-0.30462,-0.84092,0.44728,193.71,-0.66893,0.52317,0.52803,240.34
> view matrix models
> #13,-0.67804,-0.13835,-0.72189,246.5,-0.30462,-0.84092,0.44728,191.29,-0.66893,0.52317,0.52803,238.67
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.70104,-0.014048,-0.71298,249.83,-0.20116,-0.95531,0.21661,192.19,-0.68416,0.29528,0.66688,229.86
> view matrix models
> #13,-0.46429,-0.073513,-0.88263,248.77,-0.091551,-0.98723,0.13038,191.76,-0.88094,0.14134,0.45163,233.52
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.46429,-0.073513,-0.88263,249.99,-0.091551,-0.98723,0.13038,191.11,-0.88094,0.14134,0.45163,233.91
> view matrix models
> #13,-0.46429,-0.073513,-0.88263,249.11,-0.091551,-0.98723,0.13038,191.03,-0.88094,0.14134,0.45163,234.07
> view matrix models
> #13,-0.46429,-0.073513,-0.88263,248.67,-0.091551,-0.98723,0.13038,193.02,-0.88094,0.14134,0.45163,234.1
> view matrix models
> #13,-0.46429,-0.073513,-0.88263,251.38,-0.091551,-0.98723,0.13038,190.55,-0.88094,0.14134,0.45163,233.88
> view matrix models
> #13,-0.46429,-0.073513,-0.88263,250.17,-0.091551,-0.98723,0.13038,189.64,-0.88094,0.14134,0.45163,234.33
> view matrix models
> #13,-0.46429,-0.073513,-0.88263,250.45,-0.091551,-0.98723,0.13038,189.27,-0.88094,0.14134,0.45163,234.4
> view matrix models
> #13,-0.46429,-0.073513,-0.88263,247.74,-0.091551,-0.98723,0.13038,193.53,-0.88094,0.14134,0.45163,234.35
> view matrix models
> #13,-0.46429,-0.073513,-0.88263,247.69,-0.091551,-0.98723,0.13038,192.24,-0.88094,0.14134,0.45163,236.24
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.55082,0.82882,-0.098248,254.07,-0.83218,-0.53637,0.14069,213.53,0.063911,0.15925,0.98517,211.78
> view matrix models
> #13,0.75944,0.58883,-0.27664,233.75,0.23729,0.14523,0.96052,197.79,0.60576,-0.79511,-0.02943,202.51
> view matrix models
> #13,0.74537,0.30701,-0.59175,233.99,0.60394,0.064861,0.79438,194.36,0.28227,-0.94949,-0.13707,205.64
> view matrix models
> #13,0.76721,0.20518,-0.60769,231.44,0.61893,0.01172,0.78536,192.99,0.16826,-0.97865,-0.118,206.11
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.76721,0.20518,-0.60769,229.61,0.61893,0.01172,0.78536,179.46,0.16826,-0.97865,-0.118,229.88
> view matrix models
> #13,0.76721,0.20518,-0.60769,234.27,0.61893,0.01172,0.78536,182,0.16826,-0.97865,-0.118,226.23
> view matrix models
> #13,0.76721,0.20518,-0.60769,234.91,0.61893,0.01172,0.78536,182.71,0.16826,-0.97865,-0.118,224.35
> fitmap #13 inMap #2
Fit molecule fold_r_e_model_3.cif (#13) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 1780 atoms
average map value = 3.923, steps = 180
shifted from previous position = 10.3
rotated from previous position = 27.4 degrees
atoms outside contour = 1575, contour level = 9.2394
Position of fold_r_e_model_3.cif (#13) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
-0.77586550 0.61155697 0.15501870 225.53201454
0.21548834 0.48781302 -0.84593335 225.40021407
-0.59295658 -0.62292578 -0.51026069 233.77049547
Axis 0.25479180 0.85458071 -0.45251845
Axis point 119.48574199 0.00000000 151.11263225
Rotation angle (degrees) 154.04742428
Shift along axis 144.30092008
> volume #2 level 7.577
> hide #!13 models
> show #!3 models
> volume #2 style mesh
> show #!13 models
> hide #!3 models
> view matrix models
> #13,0.38547,0.30994,-0.86911,247.92,0.88664,0.1364,0.44189,179.24,0.2555,-0.94092,-0.22222,227.07
> open
> /Users/lingxiaobin/Desktop/MJB/up1-18a/alphafold3/fold_1a1_dna/fold_1a1_dna_model_0.cif
Chain information for fold_1a1_dna_model_0.cif #4
---
Chain | Description
A | .
B | .
> open
> /Users/lingxiaobin/Desktop/MJB/up1-18a/alphafold3/fold_1a1_dna/fold_1a1_dna_model_1.cif
Chain information for fold_1a1_dna_model_1.cif #5
---
Chain | Description
A | .
B | .
> open
> /Users/lingxiaobin/Desktop/MJB/up1-18a/alphafold3/fold_1a1_dna/fold_1a1_dna_model_2.cif
Chain information for fold_1a1_dna_model_2.cif #6
---
Chain | Description
A | .
B | .
> open
> /Users/lingxiaobin/Desktop/MJB/up1-18a/alphafold3/fold_1a1_dna/fold_1a1_dna_model_3.cif
Chain information for fold_1a1_dna_model_3.cif #8
---
Chain | Description
A | .
B | .
> open
> /Users/lingxiaobin/Desktop/MJB/up1-18a/alphafold3/fold_1a1_dna/fold_1a1_dna_model_4.cif
Chain information for fold_1a1_dna_model_4.cif #9
---
Chain | Description
A | .
B | .
> hide #!2 models
> hide #!13 models
> hide #5 models
> hide #6 models
> hide #8 models
> hide #9 models
> show #5 models
> hide #4 models
> show #6 models
> hide #5 models
> hide #6 models
> show #8 models
> hide #8 models
> show #9 models
> hide #9 models
> close #8-9
> close #4-6
> open
> /Users/lingxiaobin/Desktop/MJB/up1-18a/alphafold3/fold_1up1_dna/fold_1up1_dna_model_0.cif
Chain information for fold_1up1_dna_model_0.cif #4
---
Chain | Description
A | .
B | .
> open
> /Users/lingxiaobin/Desktop/MJB/up1-18a/alphafold3/fold_1up1_dna/fold_1up1_dna_model_1.cif
Chain information for fold_1up1_dna_model_1.cif #5
---
Chain | Description
A | .
B | .
> open
> /Users/lingxiaobin/Desktop/MJB/up1-18a/alphafold3/fold_1up1_dna/fold_1up1_dna_model_2.cif
Chain information for fold_1up1_dna_model_2.cif #6
---
Chain | Description
A | .
B | .
> open
> /Users/lingxiaobin/Desktop/MJB/up1-18a/alphafold3/fold_1up1_dna/fold_1up1_dna_model_3.cif
Chain information for fold_1up1_dna_model_3.cif #8
---
Chain | Description
A | .
B | .
> open
> /Users/lingxiaobin/Desktop/MJB/up1-18a/alphafold3/fold_1up1_dna/fold_1up1_dna_model_4.cif
Chain information for fold_1up1_dna_model_4.cif #9
---
Chain | Description
A | .
B | .
> hide #5 models
> hide #6 models
> hide #8 models
> hide #9 models
> show #5 models
> hide #4 models
> show #6 models
> hide #5 models
> hide #6 models
> show #8 models
> show #9 models
> hide #8 models
> hide #9 models
> close #8-9
> close #4-6
> open
> /Users/lingxiaobin/Desktop/MJB/up1-18a/alphafold3/fold_2a1_2dna/fold_2a1_2dna_model_0.cif
Chain information for fold_2a1_2dna_model_0.cif #4
---
Chain | Description
A B | .
C D | .
> open
> /Users/lingxiaobin/Desktop/MJB/up1-18a/alphafold3/fold_2a1_2dna/fold_2a1_2dna_model_1.cif
Chain information for fold_2a1_2dna_model_1.cif #5
---
Chain | Description
A B | .
C D | .
> open
> /Users/lingxiaobin/Desktop/MJB/up1-18a/alphafold3/fold_2a1_2dna/fold_2a1_2dna_model_2.cif
Chain information for fold_2a1_2dna_model_2.cif #6
---
Chain | Description
A B | .
C D | .
> open
> /Users/lingxiaobin/Desktop/MJB/up1-18a/alphafold3/fold_2a1_2dna/fold_2a1_2dna_model_3.cif
Chain information for fold_2a1_2dna_model_3.cif #8
---
Chain | Description
A B | .
C D | .
> open
> /Users/lingxiaobin/Desktop/MJB/up1-18a/alphafold3/fold_2a1_2dna/fold_2a1_2dna_model_4.cif
Chain information for fold_2a1_2dna_model_4.cif #9
---
Chain | Description
A B | .
C D | .
> hide #5 models
> hide #6 models
> hide #8 models
> hide #9 models
> show #5 models
> hide #4 models
> show #6 models
> hide #5 models
> show #8 models
> hide #6 models
> hide #8 models
> show #9 models
> close #8-9
> close #4-6
> open
> /Users/lingxiaobin/Desktop/MJB/up1-18a/alphafold3/fold_2up1_2dna/fold_2up1_2dna_model_0.cif
Chain information for fold_2up1_2dna_model_0.cif #4
---
Chain | Description
A B | .
C D | .
> open
> /Users/lingxiaobin/Desktop/MJB/up1-18a/alphafold3/fold_2up1_2dna/fold_2up1_2dna_model_1.cif
Chain information for fold_2up1_2dna_model_1.cif #5
---
Chain | Description
A B | .
C D | .
> open
> /Users/lingxiaobin/Desktop/MJB/up1-18a/alphafold3/fold_2up1_2dna/fold_2up1_2dna_model_2.cif
Chain information for fold_2up1_2dna_model_2.cif #6
---
Chain | Description
A B | .
C D | .
> open
> /Users/lingxiaobin/Desktop/MJB/up1-18a/alphafold3/fold_2up1_2dna/fold_2up1_2dna_model_3.cif
Chain information for fold_2up1_2dna_model_3.cif #8
---
Chain | Description
A B | .
C D | .
> open
> /Users/lingxiaobin/Desktop/MJB/up1-18a/alphafold3/fold_2up1_2dna/fold_2up1_2dna_model_4.cif
Chain information for fold_2up1_2dna_model_4.cif #9
---
Chain | Description
A B | .
C D | .
> hide #5 models
> hide #6 models
> hide #8 models
> hide #9 models
> show #5 models
> hide #4 models
> show #6 models
> hide #5 models
> show #8 models
> hide #6 models
> show #9 models
> hide #8 models
> close #8-9
> close #4-6
> open
> /Users/lingxiaobin/Desktop/MJB/up1-18a/alphafold3/fold_2up1_dna/fold_2up1_dna_model_0.cif
Chain information for fold_2up1_dna_model_0.cif #4
---
Chain | Description
A B | .
C | .
> close #4
> show #!1 models
> view matrix models
> #13,0.38547,0.30994,-0.86911,243.34,0.88664,0.1364,0.44189,177.37,0.2555,-0.94092,-0.22222,198.02
> close #3
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-combine-
> new-10_real_space_refined_009-coot-0.pdb
Chain information for R-combine-new-10_real_space_refined_009-coot-0.pdb #3
---
Chain | Description
A | 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
> ui tool show "Model Panel"
> select #3/C:503@C6
1 atom, 1 residue, 1 model selected
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
3324 atoms, 3716 bonds, 156 residues, 1 model selected
> select up
12029 atoms, 13466 bonds, 562 residues, 1 model selected
> style sel stick
Changed 12029 atom styles
> cartoon sel
> volume #2 level 5.06
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.62994,0.36657,0.68469,-137.11,-0.17726,0.92619,-0.33278,122.2,-0.75614,0.088268,0.64843,217.67
> view matrix models
> #3,-0.62488,0.75963,0.18024,161.92,0.13981,0.33601,-0.93142,293.17,-0.7681,-0.55683,-0.31617,546.38
> view matrix models
> #3,-0.72187,0.676,-0.14809,268.22,-0.54093,-0.68465,-0.48851,528.47,-0.43163,-0.27253,0.8599,170.75
> view matrix models
> #3,-0.24789,0.93116,-0.26738,147.65,-0.60445,-0.36434,-0.70844,530.03,-0.75709,-0.013994,0.65316,235.68
> view matrix models
> #3,-0.24837,0.93154,-0.26561,147.3,-0.60425,-0.36331,-0.70915,529.95,-0.75709,-0.015638,0.65312,235.99
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.24837,0.93154,-0.26561,151.9,-0.60425,-0.36331,-0.70915,558.07,-0.75709,-0.015638,0.65312,254.45
> view matrix models
> #3,-0.24837,0.93154,-0.26561,153.69,-0.60425,-0.36331,-0.70915,569.81,-0.75709,-0.015638,0.65312,246.16
> view matrix models
> #3,-0.24837,0.93154,-0.26561,145.7,-0.60425,-0.36331,-0.70915,559.81,-0.75709,-0.015638,0.65312,250.96
> view matrix models
> #3,-0.24837,0.93154,-0.26561,144.66,-0.60425,-0.36331,-0.70915,557.53,-0.75709,-0.015638,0.65312,255.96
> view matrix models
> #3,-0.24837,0.93154,-0.26561,127.64,-0.60425,-0.36331,-0.70915,575.72,-0.75709,-0.015638,0.65312,265.07
> view matrix models
> #3,-0.24837,0.93154,-0.26561,135.5,-0.60425,-0.36331,-0.70915,579.71,-0.75709,-0.015638,0.65312,264.96
> fitmap #3 inMap #2
Fit molecule R-combine-new-10_real_space_refined_009-coot-0.pdb (#3) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 12029 atoms
average map value = 4.84, steps = 216
shifted from previous position = 24.4
rotated from previous position = 19.1 degrees
atoms outside contour = 6256, contour level = 5.0597
Position of R-combine-new-10_real_space_refined_009-coot-0.pdb (#3) relative
to cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
0.99999992 -0.00031953 -0.00023751 0.08866704
0.00031962 0.99999987 0.00038809 -0.13025457
0.00023739 -0.00038816 0.99999990 0.03252320
Axis -0.69804943 -0.42705953 0.57475835
Axis point 0.00000000 65.30347917 321.98232720
Rotation angle (degrees) 0.03185704
Shift along axis 0.01242546
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-combine-new-11.pdb
Chain information for R-combine-new-11.pdb #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
F | No description available
G | No description available
H | No description available
I | No description available
> select #4/H:67@OP2
1 atom, 1 residue, 1 model selected
> select up
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
5810 atoms, 6509 bonds, 271 residues, 1 model selected
> select up
11963 atoms, 13391 bonds, 559 residues, 1 model selected
> style sel stick
Changed 11963 atom styles
> cartoon sel
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.088167,0.50302,0.85977,-86.379,-0.1423,0.86064,-0.48893,160.53,-0.98589,-0.079236,0.14746,404.26
> view matrix models
> #4,-0.92018,-0.32561,0.21738,415.33,0.039778,-0.63012,-0.77548,458.52,0.38948,-0.70493,0.59278,135.78
> view matrix models
> #4,-0.45821,0.87958,-0.12795,171.16,-0.30556,-0.29106,-0.9066,496.57,-0.83467,-0.37632,0.40213,372.37
> view matrix models
> #4,-0.21668,0.95482,-0.2034,122.97,-0.18164,-0.24415,-0.95258,471.86,-0.9592,-0.16945,0.22633,398.13
> view matrix models
> #4,-0.089359,0.98825,-0.12403,73.109,-0.43346,-0.1507,-0.88848,493.63,-0.89673,-0.025632,0.44183,312.3
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.089359,0.98825,-0.12403,51.284,-0.43346,-0.1507,-0.88848,509.67,-0.89673,-0.025632,0.44183,328.15
> view matrix models
> #4,-0.089359,0.98825,-0.12403,63.736,-0.43346,-0.1507,-0.88848,514.46,-0.89673,-0.025632,0.44183,331.11
> fitmap #4 inMap #2
Fit molecule R-combine-new-11.pdb (#4) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 11963 atoms
average map value = 4.79, steps = 180
shifted from previous position = 11.3
rotated from previous position = 13.8 degrees
atoms outside contour = 6282, contour level = 5.0597
Position of R-combine-new-11.pdb (#4) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 -0.00004086 -0.00004565 0.01978176
0.00004085 0.99999999 -0.00006600 0.00346270
0.00004565 0.00006600 0.99999999 -0.03683914
Axis 0.73291472 -0.50693242 0.45371305
Axis point 0.00000000 530.90737522 21.93836470
Rotation angle (degrees) 0.00515926
Shift along axis -0.00397141
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-combine-new-11-coot-0.pdb
Chain information for R-combine-new-11-coot-0.pdb #5
---
Chain | Description
A | No description available
D | No description available
F | No description available
G | No description available
H | No description available
I | No description available
> select #5/I:263@O2'
1 atom, 1 residue, 1 model selected
> select up
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
568 atoms, 638 bonds, 26 residues, 1 model selected
> select up
11985 atoms, 13419 bonds, 560 residues, 1 model selected
> style sel stick
Changed 11985 atom styles
> cartoon sel
> view matrix models #5,1,0,0,-2.4185,0,1,0,-1.6526,0,0,1,3.4752
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.0098992,0.9919,0.1266,-1.4255,-0.56818,0.098606,-0.81698,458.73,-0.82285,-0.080021,0.5626,284.14
> view matrix models
> #5,-0.27908,0.94665,0.16113,55.756,-0.66087,-0.067611,-0.74745,493.81,-0.69668,-0.31508,0.64449,283.51
> fitmap #5 inMap #2
Fit molecule R-combine-new-11-coot-0.pdb (#5) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 11985 atoms
average map value = 4.998, steps = 340
shifted from previous position = 35.5
rotated from previous position = 11.4 degrees
atoms outside contour = 6022, contour level = 5.0597
Position of R-combine-new-11-coot-0.pdb (#5) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
0.99999999 0.00001704 -0.00017603 0.02178820
-0.00001702 1.00000000 0.00010189 -0.00400511
0.00017603 -0.00010189 0.99999998 -0.01154020
Axis -0.49920520 -0.86245585 -0.08345100
Axis point 68.63390253 0.00000000 105.45349749
Rotation angle (degrees) 0.01169401
Shift along axis -0.00645951
> ui tool show "Model Panel"
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!2 models
> show #!3 models
> show #!5 models
> hide #!3 models
> view matrix models
> #5,-0.10607,0.99304,0.051115,39.738,-0.59666,-0.022439,-0.80218,509.89,-0.79546,-0.11558,0.59489,298.79
> select clear
> close #4
> close #3
> show #!1 models
> hide #!2 models
> fitmap #5 inMap #1
Fit molecule R-combine-new-11-coot-0.pdb (#5) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 11985 atoms
average map value = 3.709, steps = 212
shifted from previous position = 9.39
rotated from previous position = 23.8 degrees
atoms outside contour = 4985, contour level = 3.557
Position of R-combine-new-11-coot-0.pdb (#5) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.48324973 0.86818564 0.11279798 134.08070067
-0.60459282 -0.23775758 -0.76022290 541.77068313
-0.63319603 -0.43557436 0.63979509 315.86942909
Axis 0.19295011 0.44337064 -0.87532436
Axis point 272.28518487 308.43312429 0.00000000
Rotation angle (degrees) 122.72490876
Shift along axis -10.41210583
> hide #!1 models
> volume #1 level 4.4
> volume #1 level 4.969
> select #5/H:306
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #5/H:307
45 atoms, 49 bonds, 2 residues, 1 model selected
> select add #5/H:308
65 atoms, 70 bonds, 3 residues, 1 model selected
> select add #5/H:309
88 atoms, 95 bonds, 4 residues, 1 model selected
> select add #5/H:310
110 atoms, 119 bonds, 5 residues, 1 model selected
> select add #5/H:311
133 atoms, 144 bonds, 6 residues, 1 model selected
> select add #5/H:331
153 atoms, 165 bonds, 7 residues, 1 model selected
> select add #5/H:330
173 atoms, 186 bonds, 8 residues, 1 model selected
> select add #5/H:328
196 atoms, 211 bonds, 9 residues, 1 model selected
> select add #5/H:329
216 atoms, 232 bonds, 10 residues, 1 model selected
> select add #5/H:327
239 atoms, 257 bonds, 11 residues, 1 model selected
> select add #5/H:326
262 atoms, 282 bonds, 12 residues, 1 model selected
> volume #1 level 4.331
> select add #5/H:325
282 atoms, 303 bonds, 13 residues, 1 model selected
> select add #5/H:324
304 atoms, 327 bonds, 14 residues, 1 model selected
> select add #5/H:323
324 atoms, 348 bonds, 15 residues, 1 model selected
> select add #5/H:322
346 atoms, 372 bonds, 16 residues, 1 model selected
> select add #5/H:321
368 atoms, 396 bonds, 17 residues, 1 model selected
> select add #5/H:320
390 atoms, 420 bonds, 18 residues, 1 model selected
> select add #5/H:319
413 atoms, 445 bonds, 19 residues, 1 model selected
> select add #5/H:318
435 atoms, 469 bonds, 20 residues, 1 model selected
> select add #5/H:317
455 atoms, 490 bonds, 21 residues, 1 model selected
> select add #5/H:316
477 atoms, 514 bonds, 22 residues, 1 model selected
> select add #5/H:315
497 atoms, 535 bonds, 23 residues, 1 model selected
> select add #5/H:314
517 atoms, 556 bonds, 24 residues, 1 model selected
> select add #5/H:313
539 atoms, 580 bonds, 25 residues, 1 model selected
> select add #5/H:312
561 atoms, 604 bonds, 26 residues, 1 model selected
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R306-331.pdb models #5
> relModel #5
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R306-331.pdb
Chain information for R306-331.pdb #3
---
Chain | Description
A | No description available
D | No description available
F | No description available
G | No description available
H | No description available
I | No description available
> close #3
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R306-331.pdb models #5
> selectedOnly true relModel #5
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R306-331.pdb
Chain information for R306-331.pdb #3
---
Chain | Description
H | No description available
> delete atoms sel
> delete bonds sel
> select #3/H:315
20 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,30.92,0,1,0,11.757,0,0,1,15.143
> view matrix models #3,1,0,0,30.481,0,1,0,12.206,0,0,1,14.428
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.9876,-0.0093772,0.15673,-4.4107,-0.074947,0.849,0.52306,-76.491,-0.13797,-0.52832,0.83776,175.33
> view matrix models
> #3,0.50532,-0.81346,0.28797,200.33,-0.82692,-0.36107,0.43108,309.02,-0.24669,-0.45597,-0.85512,605.58
> view matrix models
> #3,-0.47447,-0.54088,0.6945,244.21,-0.12877,0.82312,0.55308,-68.444,-0.8708,0.17299,-0.4602,519.2
> view matrix models
> #3,-0.47154,-0.56009,0.68114,250.35,-0.15773,0.81352,0.55974,-62.701,-0.86763,0.1565,-0.47195,524.42
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.47154,-0.56009,0.68114,258.01,-0.15773,0.81352,0.55974,-60.624,-0.86763,0.1565,-0.47195,509.35
> view matrix models
> #3,-0.47154,-0.56009,0.68114,256.62,-0.15773,0.81352,0.55974,-58.461,-0.86763,0.1565,-0.47195,518.49
> view matrix models
> #3,-0.47154,-0.56009,0.68114,256.91,-0.15773,0.81352,0.55974,-55.099,-0.86763,0.1565,-0.47195,514.14
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.12986,-0.97481,0.18132,336.3,-0.39952,0.11593,0.90937,28.991,-0.90748,-0.19053,-0.3744,559.15
> view matrix models
> #3,0.13026,-0.97368,0.18703,334.6,-0.3495,0.13144,0.92767,11.842,-0.92784,-0.1862,-0.32318,549.64
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.40223,-0.45056,0.797,195.16,-0.3507,0.87995,0.32047,30.681,-0.84571,-0.1506,-0.51196,574.02
> view matrix models
> #3,-0.1011,-0.62059,0.77759,170.69,-0.51972,0.69941,0.49062,53.567,-0.84833,-0.35453,-0.39325,581.04
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.1011,-0.62059,0.77759,169.71,-0.51972,0.69941,0.49062,53.354,-0.84833,-0.35453,-0.39325,587.86
> view matrix models
> #3,-0.1011,-0.62059,0.77759,167.92,-0.51972,0.69941,0.49062,65.289,-0.84833,-0.35453,-0.39325,581.72
> view matrix models
> #3,-0.1011,-0.62059,0.77759,171.25,-0.51972,0.69941,0.49062,68.088,-0.84833,-0.35453,-0.39325,581.18
> view matrix models
> #3,-0.1011,-0.62059,0.77759,172.64,-0.51972,0.69941,0.49062,64.49,-0.84833,-0.35453,-0.39325,582.92
> ui tool show "Model Panel"
> hide #3 models
> hide #!5 models
> hide #!1 models
> show #!7 models
> close #7
> show #!10 models
> close #10
> show #11 models
> show #12 models
> hide #11 models
> close #12
> show #11 models
> hide #11 models
> show #!13 models
> select #13/A:333
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #13/A:302
40 atoms, 42 bonds, 2 residues, 1 model selected
> select add #13/A:303
60 atoms, 63 bonds, 3 residues, 1 model selected
> select add #13/A:304
80 atoms, 84 bonds, 4 residues, 1 model selected
> select add #13/A:305
103 atoms, 109 bonds, 5 residues, 1 model selected
> select add #13/A:306
125 atoms, 133 bonds, 6 residues, 1 model selected
> select add #13/A:307
145 atoms, 154 bonds, 7 residues, 1 model selected
> select add #13/A:308
168 atoms, 179 bonds, 8 residues, 1 model selected
> select add #13/A:309
190 atoms, 203 bonds, 9 residues, 1 model selected
> select add #13/A:310
213 atoms, 228 bonds, 10 residues, 1 model selected
> select add #13/A:311
235 atoms, 252 bonds, 11 residues, 1 model selected
> select add #13/A:312
257 atoms, 276 bonds, 12 residues, 1 model selected
> select add #13/A:313
277 atoms, 297 bonds, 13 residues, 1 model selected
> select add #13/A:314
297 atoms, 318 bonds, 14 residues, 1 model selected
> select add #13/A:315
319 atoms, 342 bonds, 15 residues, 1 model selected
> select add #13/A:316
339 atoms, 363 bonds, 16 residues, 1 model selected
> select add #13/A:317
361 atoms, 387 bonds, 17 residues, 1 model selected
> select add #13/A:318
384 atoms, 412 bonds, 18 residues, 1 model selected
> select add #13/A:319
406 atoms, 436 bonds, 19 residues, 1 model selected
> select add #13/A:320
428 atoms, 460 bonds, 20 residues, 1 model selected
> select add #13/A:321
450 atoms, 484 bonds, 21 residues, 1 model selected
> select add #13/A:322
470 atoms, 505 bonds, 22 residues, 1 model selected
> select add #13/A:323
492 atoms, 529 bonds, 23 residues, 1 model selected
> select add #13/A:324
512 atoms, 550 bonds, 24 residues, 1 model selected
> select add #13/A:325
535 atoms, 575 bonds, 25 residues, 1 model selected
> select add #13/A:326
558 atoms, 600 bonds, 26 residues, 1 model selected
> select add #13/A:327
581 atoms, 625 bonds, 27 residues, 1 model selected
> select add #13/A:328
601 atoms, 646 bonds, 28 residues, 1 model selected
> select add #13/A:329
621 atoms, 667 bonds, 29 residues, 1 model selected
> select add #13/A:330
641 atoms, 688 bonds, 30 residues, 1 model selected
> select add #13/A:331
663 atoms, 712 bonds, 31 residues, 1 model selected
> select add #13/A:332
685 atoms, 736 bonds, 32 residues, 1 model selected
> select ~sel & ##selected
1095 atoms, 1227 bonds, 1 pseudobond, 51 residues, 2 models selected
> delete atoms (#!13 & sel)
> delete bonds (#!13 & sel)
> show #!1 models
> show #3 models
> hide #3 models
> show #!5 models
> select #13/A:308
23 atoms, 25 bonds, 1 residue, 1 model selected
> view matrix models
> #13,0.38547,0.30994,-0.86911,248.61,0.88664,0.1364,0.44189,172.08,0.2555,-0.94092,-0.22222,229.64
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.15606,0.70676,-0.69003,257.16,0.2716,0.64096,0.71792,186.39,0.94967,-0.29945,-0.091928,232.12
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.15606,0.70676,-0.69003,250.13,0.2716,0.64096,0.71792,190.92,0.94967,-0.29945,-0.091928,229.95
> view matrix models
> #13,0.15606,0.70676,-0.69003,249.91,0.2716,0.64096,0.71792,196.25,0.94967,-0.29945,-0.091928,238.82
> view matrix models
> #13,0.15606,0.70676,-0.69003,249.52,0.2716,0.64096,0.71792,196.57,0.94967,-0.29945,-0.091928,239.22
> view matrix models
> #13,0.15606,0.70676,-0.69003,248.54,0.2716,0.64096,0.71792,202.07,0.94967,-0.29945,-0.091928,248.1
> view matrix models
> #13,0.15606,0.70676,-0.69003,255.45,0.2716,0.64096,0.71792,206.84,0.94967,-0.29945,-0.091928,239.29
> view matrix models
> #13,0.15606,0.70676,-0.69003,256.93,0.2716,0.64096,0.71792,208.18,0.94967,-0.29945,-0.091928,238.32
> view matrix models
> #13,0.15606,0.70676,-0.69003,256.93,0.2716,0.64096,0.71792,208.71,0.94967,-0.29945,-0.091928,237.22
Drag select of 492 atoms, 32 residues, 545 bonds
> delete atoms sel
> delete bonds sel
> select #5/F:365
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #5/F:366
40 atoms, 42 bonds, 2 residues, 1 model selected
> select add #5/F:367
60 atoms, 63 bonds, 3 residues, 1 model selected
> select add #5/F:368
82 atoms, 87 bonds, 4 residues, 1 model selected
> select add #5/F:369
102 atoms, 108 bonds, 5 residues, 1 model selected
> select add #5/F:370
124 atoms, 132 bonds, 6 residues, 1 model selected
> select add #5/F:371
146 atoms, 156 bonds, 7 residues, 1 model selected
> select add #5/F:404
157 atoms, 166 bonds, 8 residues, 1 model selected
> select add #5/F:405
170 atoms, 177 bonds, 9 residues, 1 model selected
> select add #5/F:406
188 atoms, 196 bonds, 10 residues, 1 model selected
> select add #5/F:407
208 atoms, 217 bonds, 11 residues, 1 model selected
> select add #5/F:408
228 atoms, 238 bonds, 12 residues, 1 model selected
> select add #5/F:409
248 atoms, 259 bonds, 13 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #5/F:364
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #5/F:363
45 atoms, 49 bonds, 2 residues, 1 model selected
> select add #5/F:360
68 atoms, 74 bonds, 3 residues, 1 model selected
> select add #5/F:359
90 atoms, 98 bonds, 4 residues, 1 model selected
> select add #5/F:416
113 atoms, 123 bonds, 5 residues, 1 model selected
> select add #5/F:415
133 atoms, 144 bonds, 6 residues, 1 model selected
> select add #5/F:414
153 atoms, 165 bonds, 7 residues, 1 model selected
> select add #5/F:413
176 atoms, 190 bonds, 8 residues, 1 model selected
> select add #5/F:412
196 atoms, 211 bonds, 9 residues, 1 model selected
> select add #5/F:411
218 atoms, 235 bonds, 10 residues, 1 model selected
> select subtract #5/F:411
196 atoms, 211 bonds, 9 residues, 1 model selected
> select add #5/F:411
218 atoms, 235 bonds, 10 residues, 1 model selected
> select add #5/F:410
240 atoms, 259 bonds, 11 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #5/F:361
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #5/F:362
40 atoms, 42 bonds, 2 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #13/A:328
20 atoms, 21 bonds, 1 residue, 1 model selected
> fitmap #13 inMap #1
Fit molecule fold_r_e_model_3.cif (#13) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 685 atoms
average map value = 2.937, steps = 104
shifted from previous position = 8
rotated from previous position = 27.9 degrees
atoms outside contour = 460, contour level = 4.3314
Position of fold_r_e_model_3.cif (#13) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.02537762 0.64482892 -0.76390552 252.04017805
-0.17215296 0.75555458 0.63206063 220.21969679
0.98474329 0.11546840 0.13018338 239.47923066
Axis -0.25855158 -0.87518913 -0.40889494
Axis point 42.13204263 0.00000000 155.75124558
Rotation angle (degrees) 92.54719018
Shift along axis -355.82111566
> view matrix models
> #13,0.025378,0.64483,-0.76391,255.1,-0.17215,0.75555,0.63206,216.95,0.98474,0.11547,0.13018,241.15
> view matrix models
> #13,0.025378,0.64483,-0.76391,257.6,-0.17215,0.75555,0.63206,214.4,0.98474,0.11547,0.13018,242.16
> view matrix models
> #13,0.025378,0.64483,-0.76391,260.57,-0.17215,0.75555,0.63206,211.58,0.98474,0.11547,0.13018,242.73
> view matrix models
> #13,0.025378,0.64483,-0.76391,264.24,-0.17215,0.75555,0.63206,207.94,0.98474,0.11547,0.13018,243.85
> view matrix models
> #13,0.025378,0.64483,-0.76391,267.53,-0.17215,0.75555,0.63206,205.04,0.98474,0.11547,0.13018,243.81
> view matrix models
> #13,0.025378,0.64483,-0.76391,271.08,-0.17215,0.75555,0.63206,201.87,0.98474,0.11547,0.13018,243.85
> select #13/A:302
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #13/A:304
60 atoms, 42 bonds, 3 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #13/A:305
23 atoms, 25 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> ui mousemode right "rotate selected models"
> select #13/A:332
22 atoms, 24 bonds, 1 residue, 1 model selected
> view matrix models
> #13,-0.12797,0.73866,-0.66182,273.71,-0.61976,0.46141,0.63482,201.64,0.77429,0.49141,0.39875,250.9
> view matrix models
> #13,-0.24442,0.60913,-0.75447,273.59,-0.96762,-0.10264,0.23061,199.17,0.063033,0.7864,0.61449,263.24
> view matrix models
> #13,0.14338,0.50596,-0.85056,267.88,-0.60804,-0.63306,-0.47908,191.69,-0.78085,0.58587,0.21687,273.57
> view matrix models
> #13,0.28506,0.44618,-0.84833,264.97,-0.086538,-0.86946,-0.48637,180.84,-0.95459,0.21206,-0.20924,272.81
> view matrix models
> #13,0.48819,0.3529,-0.79821,260.29,0.49519,-0.86513,-0.07962,170.07,-0.71865,-0.3564,-0.5971,263.06
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.48819,0.3529,-0.79821,256.19,0.49519,-0.86513,-0.07962,173.23,-0.71865,-0.3564,-0.5971,261.1
> view matrix models
> #13,0.48819,0.3529,-0.79821,255.98,0.49519,-0.86513,-0.07962,173.54,-0.71865,-0.3564,-0.5971,261.99
> view matrix models
> #13,0.48819,0.3529,-0.79821,254.44,0.49519,-0.86513,-0.07962,170.97,-0.71865,-0.3564,-0.5971,261.68
> view matrix models
> #13,0.48819,0.3529,-0.79821,253.4,0.49519,-0.86513,-0.07962,172.06,-0.71865,-0.3564,-0.5971,262.45
> view matrix models
> #13,0.48819,0.3529,-0.79821,253.19,0.49519,-0.86513,-0.07962,169.62,-0.71865,-0.3564,-0.5971,263.87
> view matrix models
> #13,0.48819,0.3529,-0.79821,253.61,0.49519,-0.86513,-0.07962,170.3,-0.71865,-0.3564,-0.5971,264.32
> select clear
> show #11 models
> hide #!5 models
> hide #!13 models
> ui tool show "Show Sequence Viewer"
> sequence chain #11/A #13/A #14/A #17/B #19/B #15/B
Alignment identifier is 1
> select #11/A #13/A #14/A #17/B #19/B #15/B
38459 atoms, 43092 bonds, 1797 residues, 6 models selected
> select clear
> select #11/A #13/A #14/A #17/B #19/B #15/B
38459 atoms, 43092 bonds, 1797 residues, 6 models selected
> select #11/A:335 #14/A:335 #17/B:335
66 atoms, 72 bonds, 3 residues, 3 models selected
> select #11/A:335 #14/A:335 #17/B:335
66 atoms, 72 bonds, 3 residues, 3 models selected
. [ID: 1] region 6 chains [335] RMSD: 80.443
> select #11/A #13/A #14/A #17/B #19/B #15/B
38459 atoms, 43092 bonds, 1797 residues, 6 models selected
> select #11/A:358 #14/A:358 #17/B:358
66 atoms, 72 bonds, 3 residues, 3 models selected
> select #11/A:358-421 #14/A:358-421 #17/B:358-421
4083 atoms, 4575 bonds, 192 residues, 3 models selected
. [ID: 1] region 6 chains [358-421] RMSD: 62.241
> select ~sel & ##selected
32953 atoms, 36921 bonds, 1540 residues, 3 models selected
> delete atoms (#11 & sel)
> delete bonds (#11 & sel)
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!13 models
Drag select of 64 residues, 128 shapes
> view matrix models #11,1,0,0,291.55,0,1,0,292.18,0,0,1,159.38
> view matrix models #11,1,0,0,288.55,0,1,0,213.91,0,0,1,255
> show #!1 models
> view matrix models #11,1,0,0,232.46,0,1,0,153.67,0,0,1,254.38
> view matrix models #11,1,0,0,238.05,0,1,0,146.07,0,0,1,295.47
> view matrix models #11,1,0,0,233.22,0,1,0,148,0,0,1,294.4
> view matrix models #11,1,0,0,252.85,0,1,0,164.51,0,0,1,326.07
> view matrix models #11,1,0,0,242.93,0,1,0,187.72,0,0,1,278.56
> view matrix models #11,1,0,0,230.81,0,1,0,191.88,0,0,1,292.24
> view matrix models #11,1,0,0,233.25,0,1,0,175.56,0,0,1,287.03
> view matrix models #11,1,0,0,231.64,0,1,0,175.49,0,0,1,286.91
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.67339,0.34672,-0.65294,225.56,-0.71869,0.09998,-0.68811,175.39,-0.1733,0.93262,0.31651,277.71
> view matrix models
> #11,0.99333,-0.071673,0.090367,232.1,0.11534,0.61352,-0.78121,186.13,0.00054953,0.78642,0.61769,280.99
> view matrix models
> #11,0.92186,-0.038919,0.38556,228.83,0.15206,0.95147,-0.26753,180.38,-0.35644,0.30526,0.88304,278.09
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.92186,-0.038919,0.38556,243.02,0.15206,0.95147,-0.26753,183.69,-0.35644,0.30526,0.88304,245.52
> view matrix models
> #11,0.92186,-0.038919,0.38556,244.32,0.15206,0.95147,-0.26753,183.34,-0.35644,0.30526,0.88304,245.02
> fitmap #11 inMap #1
Fit molecule fold_r_e_model_1.cif (#11) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 1361 atoms
average map value = 3.323, steps = 156
shifted from previous position = 7.91
rotated from previous position = 18.4 degrees
atoms outside contour = 789, contour level = 4.3314
Position of fold_r_e_model_1.cif (#11) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.79603709 0.04925729 0.60324014 235.57843635
0.03958997 0.99031072 -0.13310637 173.32450959
-0.60395164 0.12983987 0.78637397 241.24371191
Axis 0.21281978 0.97706014 -0.00782440
Axis point 458.41629743 0.00000000 -158.75874442
Rotation angle (degrees) 38.15327988
Shift along axis 217.59663427
> view matrix models
> #11,0.79604,0.049257,0.60324,232.7,0.03959,0.99031,-0.13311,175.29,-0.60395,0.12984,0.78637,244.24
> view matrix models
> #11,0.79604,0.049257,0.60324,233.51,0.03959,0.99031,-0.13311,175.81,-0.60395,0.12984,0.78637,240.88
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.5729,0.78498,0.23577,223.41,-0.44217,0.53821,-0.71751,175.13,-0.69012,0.30681,0.65543,238.09
> view matrix models
> #11,0.41043,0.91183,-0.010823,220.35,-0.50838,0.21895,-0.83283,177.86,-0.75703,0.34732,0.55342,236.96
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.41043,0.91183,-0.010823,216.56,-0.50838,0.21895,-0.83283,181.41,-0.75703,0.34732,0.55342,234.82
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.19488,0.80682,-0.55772,216.98,-0.47705,-0.41887,-0.77264,188.51,-0.857,0.41663,0.30326,233.72
> view matrix models
> #11,0.25654,0.86971,-0.42165,216.61,-0.45971,-0.27395,-0.84476,187.64,-0.85021,0.41055,0.32954,233.76
> view matrix models
> #11,0.24769,0.87394,-0.41818,216.37,-0.47664,-0.26586,-0.83793,187.19,-0.84348,0.40687,0.35071,233.8
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.24769,0.87394,-0.41818,215.3,-0.47664,-0.26586,-0.83793,187.76,-0.84348,0.40687,0.35071,232.04
> view matrix models
> #11,0.24769,0.87394,-0.41818,216.37,-0.47664,-0.26586,-0.83793,187.3,-0.84348,0.40687,0.35071,230.42
> fitmap #11 inMap #1
Fit molecule fold_r_e_model_1.cif (#11) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 1361 atoms
average map value = 3.503, steps = 328
shifted from previous position = 13.5
rotated from previous position = 37.6 degrees
atoms outside contour = 749, contour level = 4.3314
Position of fold_r_e_model_1.cif (#11) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.73813252 0.67257423 -0.05295551 233.87868063
-0.23779160 0.18590675 -0.95335923 191.83709428
-0.63136007 0.71629783 0.29715632 233.64582553
Axis 0.83998161 0.29098742 -0.45799259
Axis point 0.00000000 -144.25931629 280.06913244
Rotation angle (degrees) 83.65022311
Shift along axis 145.26791534
> hide #!1 models
> select clear
> select #11/A:402
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #11/A:403
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #11/A:376
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add #11/A:404
62 atoms, 66 bonds, 3 residues, 1 model selected
> select add #11/A:405
82 atoms, 87 bonds, 4 residues, 1 model selected
> select add #11/A:406
104 atoms, 111 bonds, 5 residues, 1 model selected
> select add #11/A:407
124 atoms, 132 bonds, 6 residues, 1 model selected
> select add #11/A:408
144 atoms, 153 bonds, 7 residues, 1 model selected
> select add #11/A:409
164 atoms, 174 bonds, 8 residues, 1 model selected
> select add #11/A:375
186 atoms, 198 bonds, 9 residues, 1 model selected
> select add #11/A:374
206 atoms, 219 bonds, 10 residues, 1 model selected
> select add #11/A:373
228 atoms, 243 bonds, 11 residues, 1 model selected
> select add #11/A:372
250 atoms, 267 bonds, 12 residues, 1 model selected
> select add #11/A:371
272 atoms, 291 bonds, 13 residues, 1 model selected
> select add #11/A:370
294 atoms, 315 bonds, 14 residues, 1 model selected
> select add #11/A:369
314 atoms, 336 bonds, 15 residues, 1 model selected
> select add #11/A:368
336 atoms, 360 bonds, 16 residues, 1 model selected
> select add #11/A:367
356 atoms, 381 bonds, 17 residues, 1 model selected
> view matrix models
> #11,0.73813,0.67257,-0.052956,234.18,-0.23779,0.18591,-0.95336,191.54,-0.63136,0.7163,0.29716,234.25
> select add #11/A:366
376 atoms, 402 bonds, 18 residues, 1 model selected
> select add #11/A:365
396 atoms, 423 bonds, 19 residues, 1 model selected
> select add #11/A:411
418 atoms, 447 bonds, 20 residues, 1 model selected
> select add #11/A:410
440 atoms, 471 bonds, 21 residues, 1 model selected
> select add #11/A:413
463 atoms, 496 bonds, 22 residues, 1 model selected
> select add #11/A:412
483 atoms, 517 bonds, 23 residues, 1 model selected
> select add #11/A:414
503 atoms, 538 bonds, 24 residues, 1 model selected
> select add #11/A:415
523 atoms, 559 bonds, 25 residues, 1 model selected
> select add #11/A:416
546 atoms, 584 bonds, 26 residues, 1 model selected
> select add #11/A:417
568 atoms, 608 bonds, 27 residues, 1 model selected
> select add #11/A:418
590 atoms, 632 bonds, 28 residues, 1 model selected
> select add #11/A:419
610 atoms, 653 bonds, 29 residues, 1 model selected
> select add #11/A:420
633 atoms, 678 bonds, 30 residues, 1 model selected
> select add #11/A:421
653 atoms, 699 bonds, 31 residues, 1 model selected
> select add #11/A:364
676 atoms, 724 bonds, 32 residues, 1 model selected
> select add #11/A:363
698 atoms, 748 bonds, 33 residues, 1 model selected
> select add #11/A:362
718 atoms, 769 bonds, 34 residues, 1 model selected
> select add #11/A:361
738 atoms, 790 bonds, 35 residues, 1 model selected
> select add #11/A:360
761 atoms, 815 bonds, 36 residues, 1 model selected
> select add #11/A:359
783 atoms, 839 bonds, 37 residues, 1 model selected
> select add #11/A:358
805 atoms, 863 bonds, 38 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #11/A:387
22 atoms, 24 bonds, 1 residue, 1 model selected
> fitmap #11 inMap #1
Fit molecule fold_r_e_model_1.cif (#11) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 556 atoms
average map value = 4.016, steps = 156
shifted from previous position = 3.16
rotated from previous position = 25.5 degrees
atoms outside contour = 259, contour level = 4.3314
Position of fold_r_e_model_1.cif (#11) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.38792224 0.90839512 -0.15599566 217.23534951
-0.30211187 -0.03458030 -0.95264506 193.06552059
-0.87077250 0.41668035 0.26102248 228.57145155
Axis 0.69775640 0.36422323 -0.61682854
Axis point 0.00000000 -124.31992430 306.74204089
Rotation angle (degrees) 101.11727307
Shift along axis 80.90690582
> select #13/A:325
23 atoms, 25 bonds, 1 residue, 1 model selected
> fitmap #13 inMap #1
Fit molecule fold_r_e_model_3.cif (#13) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 602 atoms
average map value = 3.9, steps = 184
shifted from previous position = 17.9
rotated from previous position = 36.3 degrees
atoms outside contour = 305, contour level = 4.3314
Position of fold_r_e_model_3.cif (#13) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.90081659 0.26383568 -0.34484810 228.11462093
0.32857244 -0.93341062 0.14416922 165.60943495
-0.28384789 -0.24317760 -0.92752091 262.72564372
Axis -0.97463266 -0.15348723 0.16288907
Axis point 0.00000000 80.08793942 143.51826262
Rotation angle (degrees) 168.53821742
Shift along axis -204.95175822
> view matrix models
> #13,0.90082,0.26384,-0.34485,241.12,0.32857,-0.93341,0.14417,168.37,-0.28385,-0.24318,-0.92752,257.41
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.048405,0.5231,-0.8509,261.28,-0.44888,-0.74963,-0.48638,187.23,-0.89228,0.40549,0.19852,266.01
> view matrix models
> #13,0.32966,0.66655,-0.6686,258.77,0.15907,-0.73728,-0.65659,181.62,-0.9306,0.1101,-0.34908,266.28
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.32966,0.66655,-0.6686,258.1,0.15907,-0.73728,-0.65659,187.09,-0.9306,0.1101,-0.34908,272.62
> view matrix models
> #13,0.32966,0.66655,-0.6686,259.51,0.15907,-0.73728,-0.65659,188.01,-0.9306,0.1101,-0.34908,269.98
> view matrix models
> #13,0.32966,0.66655,-0.6686,259.37,0.15907,-0.73728,-0.65659,189.15,-0.9306,0.1101,-0.34908,269.86
> view matrix models
> #13,0.32966,0.66655,-0.6686,259.37,0.15907,-0.73728,-0.65659,188.41,-0.9306,0.1101,-0.34908,271.53
> view matrix models
> #13,0.32966,0.66655,-0.6686,260.17,0.15907,-0.73728,-0.65659,189.35,-0.9306,0.1101,-0.34908,273.19
> view matrix models
> #13,0.32966,0.66655,-0.6686,261.35,0.15907,-0.73728,-0.65659,187.63,-0.9306,0.1101,-0.34908,274.69
> view matrix models
> #13,0.32966,0.66655,-0.6686,261.88,0.15907,-0.73728,-0.65659,187.97,-0.9306,0.1101,-0.34908,274.54
> view matrix models
> #13,0.32966,0.66655,-0.6686,262.25,0.15907,-0.73728,-0.65659,188.07,-0.9306,0.1101,-0.34908,274.61
> view matrix models
> #13,0.32966,0.66655,-0.6686,262.56,0.15907,-0.73728,-0.65659,188.11,-0.9306,0.1101,-0.34908,273.45
> view matrix models
> #13,0.32966,0.66655,-0.6686,262.25,0.15907,-0.73728,-0.65659,186.84,-0.9306,0.1101,-0.34908,274.23
> view matrix models
> #13,0.32966,0.66655,-0.6686,262.26,0.15907,-0.73728,-0.65659,186.94,-0.9306,0.1101,-0.34908,274
> select #5/I:251
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #5/I:253
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #5/I:254
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/I:253
23 atoms, 25 bonds, 1 residue, 1 model selected
> view matrix models
> #5,-0.48325,0.86819,0.1128,134.2,-0.60459,-0.23776,-0.76022,541.24,-0.6332,-0.43557,0.6398,316.44
> ui mousemode right "translate selected atoms"
> select #5/I:252
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #5/I:251
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #5/I:252
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #5/I:253
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #5/I:252
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #5/I:251
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #5/I:253
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #5/I:253
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #5/I:252
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #5/I:251
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #5/I:252
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #5/I:253
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #5/A:1
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #5/H:298
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #5/H:297
40 atoms, 42 bonds, 2 residues, 1 model selected
> select add #5/H:296
62 atoms, 66 bonds, 3 residues, 1 model selected
> select clear
> select add #5/H:297
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #5/H:296
42 atoms, 45 bonds, 2 residues, 1 model selected
> select clear
> select #5/H:296
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #5/H:218
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #5/H:217
42 atoms, 45 bonds, 2 residues, 1 model selected
> select subtract #5/H:218
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #5/H:218
42 atoms, 45 bonds, 2 residues, 1 model selected
> select clear
> select #5/H:218
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/H:297
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/H:298
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/H:297
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/H:298
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/H:297
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/H:296
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #5/H:218
20 atoms, 21 bonds, 1 residue, 1 model selected
> open
> /Users/lingxiaobin/Desktop/fold_2024_07_24_00_00/fold_2024_07_24_00_00_model_0.cif
Chain information for fold_2024_07_24_00_00_model_0.cif #4
---
Chain | Description
A | .
> open
> /Users/lingxiaobin/Desktop/fold_2024_07_24_00_00/fold_2024_07_24_00_00_model_1.cif
Chain information for fold_2024_07_24_00_00_model_1.cif #6
---
Chain | Description
A | .
> open
> /Users/lingxiaobin/Desktop/fold_2024_07_24_00_00/fold_2024_07_24_00_00_model_2.cif
Chain information for fold_2024_07_24_00_00_model_2.cif #7
---
Chain | Description
A | .
> open
> /Users/lingxiaobin/Desktop/fold_2024_07_24_00_00/fold_2024_07_24_00_00_model_3.cif
Chain information for fold_2024_07_24_00_00_model_3.cif #8
---
Chain | Description
A | .
> open
> /Users/lingxiaobin/Desktop/fold_2024_07_24_00_00/fold_2024_07_24_00_00_model_4.cif
Chain information for fold_2024_07_24_00_00_model_4.cif #9
---
Chain | Description
A | .
> hide #6 models
> hide #7 models
> hide #8 models
> hide #9 models
> hide #11 models
> hide #!13 models
Drag select of 22 residues, 66 shapes
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,-89.439,0,1,0,67.511,0,0,1,308.24
> view matrix models #4,1,0,0,214.37,0,1,0,271.76,0,0,1,186.97
> view matrix models #4,1,0,0,245.57,0,1,0,209.24,0,0,1,284.73
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.12355,-0.98914,0.079575,245.14,0.87062,-0.069562,0.48702,210.02,-0.4762,0.12945,0.86976,284.37
> view matrix models
> #4,-0.83034,-0.19746,0.5211,246.37,0.39886,0.44245,0.80321,210.84,-0.38916,0.87478,-0.28863,282.46
> view matrix models
> #4,-0.52007,0.42818,0.73905,247,0.76991,0.60965,0.18859,209.68,-0.36981,0.66708,-0.64672,281.68
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.52007,0.42818,0.73905,220.42,0.76991,0.60965,0.18859,257.73,-0.36981,0.66708,-0.64672,268.04
> view matrix models
> #4,-0.52007,0.42818,0.73905,217.46,0.76991,0.60965,0.18859,262.95,-0.36981,0.66708,-0.64672,266.15
> hide #4 models
> show #6 models
> hide #!5 models
> show #7 models
> hide #6 models
> show #6 models
> hide #7 models
> hide #6 models
> show #7 models
> show #8 models
> hide #7 models
> hide #8 models
> show #9 models
Drag select of 22 residues, 66 shapes
> show #!5 models
> view matrix models #9,1,0,0,160.61,0,1,0,56.207,0,0,1,359.08
> view matrix models #9,1,0,0,279.79,0,1,0,231.97,0,0,1,278.57
> view matrix models #9,1,0,0,243.69,0,1,0,221.21,0,0,1,245.67
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #11 models
> show #!13 models
> view matrix models #9,1,0,0,200.32,0,1,0,209.78,0,0,1,269.93
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.019221,-0.99899,-0.040494,201.25,0.55867,-0.022858,0.82907,205.98,-0.82916,-0.038558,0.55767,272.42
> view matrix models
> #9,0.29128,-0.90268,0.31675,200.36,0.61317,0.43032,0.66245,206.78,-0.73428,0.0012611,0.67884,272.15
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.29128,-0.90268,0.31675,185.13,0.61317,0.43032,0.66245,240.96,-0.73428,0.0012611,0.67884,268.68
> view matrix models
> #9,0.29128,-0.90268,0.31675,182.93,0.61317,0.43032,0.66245,240.47,-0.73428,0.0012611,0.67884,265.18
> view matrix models
> #9,0.29128,-0.90268,0.31675,182.45,0.61317,0.43032,0.66245,240.79,-0.73428,0.0012611,0.67884,264.3
> view matrix models
> #9,0.29128,-0.90268,0.31675,183.02,0.61317,0.43032,0.66245,240.57,-0.73428,0.0012611,0.67884,264.97
> show #4 models
> fitmap #9 inMap #1
Fit molecule fold_2024_07_24_00_00_model_4.cif (#9) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 475 atoms
average map value = 3.709, steps = 160
shifted from previous position = 9.38
rotated from previous position = 39.7 degrees
atoms outside contour = 248, contour level = 4.3314
Position of fold_2024_07_24_00_00_model_4.cif (#9) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.36315455 -0.92335959 0.12460277 191.71396872
0.92187480 0.37548460 0.09569836 240.44576523
-0.13515042 0.08011486 0.98758087 260.75085779
Axis -0.00836252 0.13939052 0.99020218
Axis point -50.79123153 245.28491204 0.00000000
Rotation angle (degrees) 68.70868451
Shift along axis 290.10871394
> select #4/A:6
22 atoms, 24 bonds, 1 residue, 1 model selected
> view matrix models
> #4,-0.52007,0.42818,0.73905,189.89,0.76991,0.60965,0.18859,247.89,-0.36981,0.66708,-0.64672,249.24
> view matrix models
> #4,-0.52007,0.42818,0.73905,196.93,0.76991,0.60965,0.18859,240.4,-0.36981,0.66708,-0.64672,259.16
> fitmap #4 inMap #1
Fit molecule fold_2024_07_24_00_00_model_0.cif (#4) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 475 atoms
average map value = 3.75, steps = 140
shifted from previous position = 3.68
rotated from previous position = 71.6 degrees
atoms outside contour = 257, contour level = 4.3314
Position of fold_2024_07_24_00_00_model_0.cif (#4) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.14398182 -0.44377865 0.88449406 196.05124852
0.96677063 0.25387948 -0.02999579 241.18020947
-0.21124340 0.85942173 0.46558620 260.51866126
Axis 0.44574894 0.54915020 0.70692428
Axis point 3.12732256 29.95027363 0.00000000
Rotation angle (degrees) 93.91498689
Shift along axis 404.00076386
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #9 models
> show #9 models
> close #4
> hide #9 models
Drag select of 86 atoms, 7 residues, 97 bonds
> delete atoms sel
> delete bonds sel
Drag select of 44 atoms, 2 residues, 1 pseudobonds, 48 bonds
> delete atoms (#!5 & sel)
> delete bonds (#!5 & sel)
> show #9 models
> open
> /Users/lingxiaobin/Desktop/fold_2024_07_24_00_10/fold_2024_07_24_00_10_model_0.cif
Chain information for fold_2024_07_24_00_10_model_0.cif #4
---
Chain | Description
A | .
> open
> /Users/lingxiaobin/Desktop/fold_2024_07_24_00_10/fold_2024_07_24_00_10_model_1.cif
Chain information for fold_2024_07_24_00_10_model_1.cif #10
---
Chain | Description
A | .
> open
> /Users/lingxiaobin/Desktop/fold_2024_07_24_00_10/fold_2024_07_24_00_10_model_2.cif
Chain information for fold_2024_07_24_00_10_model_2.cif #12
---
Chain | Description
A | .
> open
> /Users/lingxiaobin/Desktop/fold_2024_07_24_00_10/fold_2024_07_24_00_10_model_3.cif
Chain information for fold_2024_07_24_00_10_model_3.cif #16
---
Chain | Description
A | .
> open
> /Users/lingxiaobin/Desktop/fold_2024_07_24_00_10/fold_2024_07_24_00_10_model_4.cif
Chain information for fold_2024_07_24_00_10_model_4.cif #18
---
Chain | Description
A | .
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #!1 models
> hide #!5 models
> hide #9 models
> hide #10 models
> show #10 models
> hide #4 models
> show #4 models
> hide #4 models
> hide #10 models
> hide #11 models
> hide #12 models
> hide #!13 models
> show #4 models
> hide #16 models
> hide #18 models
> show #10 models
> hide #4 models
> close #4
> show #12 models
> hide #10 models
> show #10 models
> hide #12 models
> hide #10 models
> show #12 models
> show #16 models
> hide #12 models
> show #18 models
> hide #16 models
> close #18
> close #16
> show #10 models
> close #12
Drag select of 31 residues, 93 shapes
> show #!1 models
> show #!5 models
> view matrix models #10,1,0,0,194.14,0,1,0,299.41,0,0,1,384.01
> view matrix models #10,1,0,0,209.8,0,1,0,246.71,0,0,1,297.53
> view matrix models #10,1,0,0,166.93,0,1,0,254.17,0,0,1,276.73
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.38584,0.88383,0.26453,172.11,-0.87884,-0.26489,-0.39683,250.22,-0.28066,-0.38559,0.87895,275.4
> view matrix models
> #10,-0.96389,0.25973,0.058813,170.09,-0.26246,-0.88914,-0.37488,247.51,-0.045074,-0.37678,0.92521,275.34
> view matrix models
> #10,-0.8329,0.52853,-0.1641,170.18,-0.49758,-0.84499,-0.196,248.72,-0.24225,-0.081593,0.96678,276.74
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.8329,0.52853,-0.1641,186.11,-0.49758,-0.84499,-0.196,218.37,-0.24225,-0.081593,0.96678,298.11
> view matrix models
> #10,-0.8329,0.52853,-0.1641,187.72,-0.49758,-0.84499,-0.196,220.2,-0.24225,-0.081593,0.96678,294.36
> fitmap #10 inMap #1
Fit molecule fold_2024_07_24_00_10_model_1.cif (#10) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 670 atoms
average map value = 3.082, steps = 156
shifted from previous position = 8.74
rotated from previous position = 38.3 degrees
atoms outside contour = 415, contour level = 4.3314
Position of fold_2024_07_24_00_10_model_1.cif (#10) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.61087475 0.66187014 0.43446514 194.59674771
-0.78265881 -0.58764944 -0.20521530 224.25171490
0.11948732 -0.46539882 0.87699870 298.22551480
Axis -0.17331822 0.20981881 -0.96225613
Axis point 136.58827762 110.07808425 0.00000000
Rotation angle (degrees) 131.35806996
Shift along axis -273.64426489
> view matrix models
> #10,-0.61087,0.66187,0.43447,195.27,-0.78266,-0.58765,-0.20522,223.98,0.11949,-0.4654,0.877,298.77
> fitmap #10 inMap #1
Fit molecule fold_2024_07_24_00_10_model_1.cif (#10) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 670 atoms
average map value = 3.082, steps = 68
shifted from previous position = 0.906
rotated from previous position = 0.0665 degrees
atoms outside contour = 415, contour level = 4.3314
Position of fold_2024_07_24_00_10_model_1.cif (#10) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.61011404 0.66203957 0.43527515 194.59298573
-0.78314945 -0.58721561 -0.20458440 224.24712603
0.12015740 -0.46570531 0.87674441 298.22605124
Axis -0.17384686 0.20979642 -0.96216565
Axis point 136.56482348 110.08157520 0.00000000
Rotation angle (degrees) 131.32219336
Shift along axis -273.72599671
> show #6 models
> hide #6 models
> show #!13 models
> show #11 models
> show #25 models
> hide #25 models
> close #3
> show #6 models
> hide #6 models
> show #7 models
> hide #7 models
> show #8 models
> hide #8 models
> show #9 models
> close #8
> close #7
> close #6
> hide #10 models
> show #10 models
> open
> /Users/lingxiaobin/Desktop/fold_2024_07_24_00_12/fold_2024_07_24_00_12_model_0.cif
Chain information for fold_2024_07_24_00_12_model_0.cif #3
---
Chain | Description
A | .
> open
> /Users/lingxiaobin/Desktop/fold_2024_07_24_00_12/fold_2024_07_24_00_12_model_1.cif
Chain information for fold_2024_07_24_00_12_model_1.cif #4
---
Chain | Description
A | .
> open
> /Users/lingxiaobin/Desktop/fold_2024_07_24_00_12/fold_2024_07_24_00_12_model_2.cif
Chain information for fold_2024_07_24_00_12_model_2.cif #6
---
Chain | Description
A | .
> open
> /Users/lingxiaobin/Desktop/fold_2024_07_24_00_12/fold_2024_07_24_00_12_model_3.cif
Chain information for fold_2024_07_24_00_12_model_3.cif #7
---
Chain | Description
A | .
> open
> /Users/lingxiaobin/Desktop/fold_2024_07_24_00_12/fold_2024_07_24_00_12_model_4.cif
Chain information for fold_2024_07_24_00_12_model_4.cif #8
---
Chain | Description
A | .
> hide #4 models
> hide #6 models
> hide #7 models
> hide #8 models
Drag select of 21 residues, 61 shapes
> view matrix models #3,1,0,0,1.6777,0,1,0,19.927,0,0,1,57.188
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.08017,-0.8385,0.53898,-1.5718,-0.43937,0.45563,0.77418,17.349,-0.89472,-0.29888,-0.33189,57.503
> view matrix models
> #3,-0.86448,-0.44353,0.23654,-2.5357,-0.48321,0.86292,-0.14794,19.566,-0.1385,-0.24219,-0.96029,60.382
> view matrix models
> #3,-0.83371,-0.38132,0.39941,-3.0166,-0.38278,0.92039,0.079721,19.242,-0.39801,-0.086422,-0.9133,59.91
> view matrix models
> #3,-0.65555,-0.14764,0.74057,-3.3931,-0.034236,0.9855,0.16616,19.524,-0.75437,0.083574,-0.65111,59.022
> show #6 models
> show #4 models
> hide #6 models
> view matrix models
> #3,-0.65474,-0.14893,0.74104,-3.3941,-0.034155,0.98522,0.16783,19.521,-0.75508,0.084573,-0.65015,59.02
> view matrix models
> #3,-0.75423,-0.18385,0.63035,-3.3472,-0.13631,0.98293,0.12358,19.458,-0.64231,0.0072871,-0.76641,59.352
> select #4/A:24
23 atoms, 25 bonds, 1 residue, 1 model selected
> view matrix models
> #4,0.4551,0.23702,0.85831,-0.98735,-0.84944,0.40467,0.33865,-0.94095,-0.26707,-0.88321,0.3855,0.12835
> view matrix models
> #4,0.067452,-0.87273,0.48352,-1.0476,-0.30079,-0.47987,-0.82417,0.44372,0.9513,-0.089847,-0.29488,1.6634
> view matrix models
> #4,-0.895,-0.44214,-0.059112,-0.67588,-0.091677,0.31201,-0.94565,0.76974,0.43655,-0.84093,-0.31978,1.3764
> view matrix models
> #4,-0.72135,-0.69096,-0.047257,-0.65664,0.028204,0.03887,-0.99885,0.82926,0.692,-0.72185,-0.0085513,1.2468
> view matrix models
> #4,-0.7182,-0.6748,-0.16979,-0.50108,0.2057,0.027202,-0.97824,0.89736,0.66473,-0.7375,0.11927,1.1662
> view matrix models
> #4,-0.7631,-0.63198,-0.13519,-0.55949,0.13983,0.042774,-0.98925,0.87502,0.63097,-0.7738,0.055727,1.2197
> view matrix models
> #4,-0.7985,-0.58698,-0.13364,-0.57688,0.10948,0.076703,-0.99103,0.86289,0.59196,-0.80596,0.0030147,1.2538
> view matrix models
> #4,-0.82288,-0.54865,-0.14781,-0.57145,0.10462,0.1094,-0.98848,0.86045,0.5585,-0.82887,-0.032628,1.2717
> select #3/A:5
23 atoms, 25 bonds, 1 residue, 1 model selected
> view matrix models
> #3,0.45735,0.4735,0.75275,-0.402,0.46383,0.5952,-0.6562,22.38,-0.75875,0.64926,0.052586,57.658
> view matrix models
> #3,0.92659,0.3668,0.082963,1.54,0.0094311,0.19787,-0.98018,21.929,-0.37595,0.90901,0.17989,58.221
> view matrix models
> #3,0.95431,0.29812,-0.020142,1.7405,-0.062233,0.13238,-0.98924,21.726,-0.29225,0.9453,0.14488,58.512
Drag select of 8 residues, 18 shapes
> view matrix models
> #3,0.89215,0.41638,0.17519,1.34,-0.015168,0.41522,-0.9096,21.87,-0.45148,0.80884,0.37675,57.446
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.89215,0.41638,0.17519,2.0185,-0.015168,0.41522,-0.9096,131.67,-0.45148,0.80884,0.37675,312.8
> view matrix models
> #3,0.89215,0.41638,0.17519,163.78,-0.015168,0.41522,-0.9096,159.93,-0.45148,0.80884,0.37675,415.4
> view matrix models
> #3,0.89215,0.41638,0.17519,163.52,-0.015168,0.41522,-0.9096,248.74,-0.45148,0.80884,0.37675,269.87
> select #10/A:28
22 atoms, 24 bonds, 1 residue, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.61456,0.65886,0.43385,194.58,-0.77962,-0.59125,-0.20646,224.22,0.12049,-0.46511,0.87701,298.23
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.61456,0.65886,0.43385,181.38,-0.77962,-0.59125,-0.20646,249.66,0.12049,-0.46511,0.87701,281.82
> select #3/A:18
20 atoms, 21 bonds, 1 residue, 1 model selected
> view matrix models
> #3,0.89215,0.41638,0.17519,181.39,-0.015168,0.41522,-0.9096,218.48,-0.45148,0.80884,0.37675,304.77
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.61199,0.045362,0.78956,177.01,-0.15,0.97358,-0.1722,216.75,-0.77651,-0.22381,-0.58901,305.91
> view matrix models
> #3,-0.48869,0.055912,0.87066,177.07,-0.43166,0.85175,-0.29698,216.42,-0.75819,-0.52096,-0.39211,305.31
> view matrix models
> #3,-0.77339,0.13499,0.61939,177.19,0.29746,0.9401,0.16653,216.8,-0.5598,0.31304,-0.76722,307.28
> fitmap #3 inMap #1
Fit molecule fold_2024_07_24_00_12_model_0.cif (#3) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 537 atoms
average map value = 3.48, steps = 368
shifted from previous position = 18.1
rotated from previous position = 32.3 degrees
atoms outside contour = 295, contour level = 4.3314
Position of fold_2024_07_24_00_12_model_0.cif (#3) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.79958057 0.18418763 0.57161686 189.83562000
0.54147065 0.63280079 0.55350944 225.27325013
-0.25977001 0.75208914 -0.60570741 316.75024116
Axis 0.21434731 0.89740057 0.38565197
Axis point 92.09367241 0.00000000 94.70069637
Rotation angle (degrees) 152.40494893
Shift along axis 365.00645281
> select #1
2 models selected
> select clear
> select #3/A:20
22 atoms, 24 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.79958,0.18419,0.57162,191.03,0.54147,0.6328,0.55351,217.86,-0.25977,0.75209,-0.60571,302.64
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.7585,-0.14938,0.63432,190.87,0.097989,0.93616,0.33763,217.36,-0.64427,0.31825,-0.69544,301.72
> view matrix models
> #3,-0.80912,-0.21157,0.54823,190.88,-0.078217,0.96341,0.25635,217.23,-0.58241,0.16454,-0.79607,301.87
> fitmap #3 inMap #1
Fit molecule fold_2024_07_24_00_12_model_0.cif (#3) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 537 atoms
average map value = 3.205, steps = 176
shifted from previous position = 8.97
rotated from previous position = 42.7 degrees
atoms outside contour = 325, contour level = 4.3314
Position of fold_2024_07_24_00_12_model_0.cif (#3) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.84402259 -0.52537755 -0.10772330 194.47128117
-0.52564935 0.77054396 0.36049241 225.30352311
-0.10638909 0.36088842 -0.92652087 303.83405667
Axis 0.27926575 -0.94088846 -0.19167561
Axis point 130.62244474 0.00000000 129.01586869
Rotation angle (degrees) 179.95937638
Shift along axis -215.91389644
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.84402,-0.52538,-0.10772,197.92,-0.52565,0.77054,0.36049,217.64,-0.10639,0.36089,-0.92652,297.2
> view matrix models
> #3,-0.84402,-0.52538,-0.10772,196.95,-0.52565,0.77054,0.36049,219.61,-0.10639,0.36089,-0.92652,296.35
> view matrix models
> #3,-0.84402,-0.52538,-0.10772,197.34,-0.52565,0.77054,0.36049,218.33,-0.10639,0.36089,-0.92652,293.69
> view matrix models
> #3,-0.84402,-0.52538,-0.10772,195.31,-0.52565,0.77054,0.36049,221.5,-0.10639,0.36089,-0.92652,291.11
> view matrix models
> #3,-0.84402,-0.52538,-0.10772,197.06,-0.52565,0.77054,0.36049,217.02,-0.10639,0.36089,-0.92652,291.6
> fitmap #3 inMap #1
Fit molecule fold_2024_07_24_00_12_model_0.cif (#3) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 537 atoms
average map value = 3.546, steps = 148
shifted from previous position = 2.27
rotated from previous position = 21.9 degrees
atoms outside contour = 299, contour level = 4.3314
Position of fold_2024_07_24_00_12_model_0.cif (#3) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.76578885 -0.61926528 -0.17342995 197.93409772
-0.56494091 0.51895212 0.64150641 218.88572578
-0.30726081 0.58923613 -0.74725604 291.86945676
Axis -0.34029366 0.87127512 0.35366636
Axis point 146.38508250 0.00000000 95.43988212
Rotation angle (degrees) 175.59524789
Shift along axis 226.57837696
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.61593,-0.62011,-0.4859,198.85,-0.77638,0.37312,0.50795,218.58,-0.13368,0.69011,-0.71125,292.25
> select #1
2 models selected
> select clear
> select #10/A:25
23 atoms, 25 bonds, 1 residue, 1 model selected
> view matrix models
> #10,-0.8284,0.022309,-0.5597,176.01,0.26691,-0.86275,-0.42944,246.49,-0.49246,-0.50514,0.70875,281.85
> view matrix models
> #10,-0.88056,0.055941,-0.47062,176.54,0.19062,-0.86735,-0.45976,246.45,-0.43391,-0.49455,0.75309,281.98
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.88056,0.055941,-0.47062,174.07,0.19062,-0.86735,-0.45976,251.59,-0.43391,-0.49455,0.75309,279.88
> view matrix models
> #10,-0.88056,0.055941,-0.47062,175.3,0.19062,-0.86735,-0.45976,254.19,-0.43391,-0.49455,0.75309,275.3
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.18853,0.043078,-0.98112,172.22,0.76014,-0.62615,-0.17356,255.17,-0.6218,-0.77851,0.085304,272.32
> view matrix models
> #10,-0.85983,-0.18382,-0.47634,174.45,0.46591,-0.66409,-0.58474,254.18,-0.20884,-0.7247,0.65665,274.09
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.85983,-0.18382,-0.47634,175.37,0.46591,-0.66409,-0.58474,253.33,-0.20884,-0.7247,0.65665,277.59
> view matrix models
> #10,-0.85983,-0.18382,-0.47634,181.43,0.46591,-0.66409,-0.58474,252.36,-0.20884,-0.7247,0.65665,278.28
> view matrix models
> #10,-0.85983,-0.18382,-0.47634,181.2,0.46591,-0.66409,-0.58474,255.18,-0.20884,-0.7247,0.65665,276.21
> fitmap #10 inMap #1
Fit molecule fold_2024_07_24_00_10_model_1.cif (#10) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 670 atoms
average map value = 4.072, steps = 180
shifted from previous position = 7.25
rotated from previous position = 37.2 degrees
atoms outside contour = 316, contour level = 4.3314
Position of fold_2024_07_24_00_10_model_1.cif (#10) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.46364094 -0.14145913 -0.87465787 187.43976046
0.56291215 -0.80936824 -0.16749016 253.53641587
-0.68422729 -0.57001084 0.45488531 272.84492349
Axis -0.48303137 -0.22851979 0.84525700
Axis point 136.52350975 192.97304945 0.00000000
Rotation angle (degrees) 155.37603783
Shift along axis 82.14670946
> hide #3 models
> show #3 models
> hide #4 models
> show #4 models
> close #4
> close #3
> hide #9 models
> show #9 models
> hide #10 models
> close #10
> open
> /Users/lingxiaobin/Downloads/fold_2024_07_24_00_24/fold_2024_07_24_00_24_model_0.cif
Chain information for fold_2024_07_24_00_24_model_0.cif #3
---
Chain | Description
A | .
Drag select of 24 residues, 72 shapes
> view matrix models #3,1,0,0,-16.388,0,1,0,247.86,0,0,1,296.72
> view matrix models #3,1,0,0,185.4,0,1,0,385.48,0,0,1,282.27
> view matrix models #3,1,0,0,171.5,0,1,0,272.74,0,0,1,298.62
> view matrix models #3,1,0,0,232.44,0,1,0,280,0,0,1,296
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.5702,0.037274,0.82066,226.64,-0.81491,-0.152,-0.5593,277.76,0.10389,-0.98768,0.11705,296.95
> view matrix models
> #3,-0.82183,-0.23843,-0.51744,226.24,0.4758,0.21233,-0.85354,282.53,0.31338,-0.94766,-0.061053,297.87
> view matrix models
> #3,-0.66189,0.5287,-0.53139,226.63,0.73661,0.59015,-0.33034,283.17,0.13895,-0.61008,-0.78006,298.01
> view matrix models
> #3,-0.34231,0.39854,-0.85088,228.19,0.90792,0.37344,-0.19034,283.64,0.2419,-0.83768,-0.48967,297.91
> view matrix models
> #3,-0.50578,0.4126,-0.7576,227.43,0.82451,0.48951,-0.28385,283.44,0.25374,-0.7682,-0.58778,298.05
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.50578,0.4126,-0.7576,229.26,0.82451,0.48951,-0.28385,273.24,0.25374,-0.7682,-0.58778,277.42
> view matrix models
> #3,-0.50578,0.4126,-0.7576,172.61,0.82451,0.48951,-0.28385,248.25,0.25374,-0.7682,-0.58778,280.18
> view matrix models
> #3,-0.50578,0.4126,-0.7576,174.02,0.82451,0.48951,-0.28385,248.89,0.25374,-0.7682,-0.58778,281.87
> view matrix models
> #3,-0.50578,0.4126,-0.7576,176.96,0.82451,0.48951,-0.28385,254.11,0.25374,-0.7682,-0.58778,276.78
> fitmap #3 inMap #1
Fit molecule fold_2024_07_24_00_24_model_0.cif (#3) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 521 atoms
average map value = 4.189, steps = 140
shifted from previous position = 9.24
rotated from previous position = 25.3 degrees
atoms outside contour = 227, contour level = 4.3314
Position of fold_2024_07_24_00_24_model_0.cif (#3) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.54409587 0.71214428 -0.44363296 186.14499858
0.83875665 0.44834675 -0.30898620 254.30058657
-0.02114136 -0.54021821 -0.84125937 279.32548224
Axis -0.46432685 -0.84838682 0.25424474
Axis point -1.72188484 0.00000000 183.64234518
Rotation angle (degrees) 165.58183033
Shift along axis -231.16035064
> open
> /Users/lingxiaobin/Desktop/fold_2024_07_24_00_25/fold_2024_07_24_00_25_model_0.cif
Chain information for fold_2024_07_24_00_25_model_0.cif #4
---
Chain | Description
A | .
Drag select of 32 residues, 96 shapes
> view matrix models #4,1,0,0,234.47,0,1,0,189.79,0,0,1,307.33
> view matrix models #4,1,0,0,197.82,0,1,0,220.3,0,0,1,275.01
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.70596,-0.43866,0.55606,196.96,-0.284,-0.89456,-0.34513,225.68,0.64882,0.085728,-0.7561,281.12
> view matrix models
> #4,0.80327,0.41703,0.42525,196.22,0.37095,-0.90888,0.1906,224.44,0.46599,0.0046436,-0.88478,281.43
> view matrix models
> #4,0.91741,0.39382,0.057205,197.59,0.35844,-0.88018,0.31113,224.08,0.17288,-0.26493,-0.94864,281.71
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.91741,0.39382,0.057205,200.75,0.35844,-0.88018,0.31113,227.81,0.17288,-0.26493,-0.94864,296.62
> view matrix models
> #4,0.91741,0.39382,0.057205,200.94,0.35844,-0.88018,0.31113,226.98,0.17288,-0.26493,-0.94864,295.47
> fitmap #4 inMap #1
Fit molecule fold_2024_07_24_00_25_model_0.cif (#4) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 686 atoms
average map value = 3.805, steps = 608
shifted from previous position = 9.17
rotated from previous position = 71.4 degrees
atoms outside contour = 348, contour level = 4.3314
Position of fold_2024_07_24_00_25_model_0.cif (#4) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.10424048 0.81369548 -0.57186849 194.19871519
0.86556795 -0.35741522 -0.35077982 226.79853857
-0.48982246 -0.45842559 -0.74156587 302.27728080
Axis -0.74265105 -0.56603781 0.35786954
Axis point 0.00000000 48.21339452 194.66209873
Rotation angle (degrees) 175.84390269
Shift along axis -164.42259605
> open
> /Users/lingxiaobin/Desktop/fold_2024_07_24_00_25/fold_2024_07_24_00_25_model_1.cif
Chain information for fold_2024_07_24_00_25_model_1.cif #10
---
Chain | Description
A | .
Drag select of 32 residues, 96 shapes
> view matrix models #10,1,0,0,173.69,0,1,0,319.11,0,0,1,33.346
> view matrix models #10,1,0,0,172.48,0,1,0,257.84,0,0,1,307
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.63976,0.22184,0.73586,173.04,0.61947,0.41789,-0.66455,256.55,-0.45493,0.881,0.12993,307.03
> open
> /Users/lingxiaobin/Desktop/fold_2024_07_24_00_25/fold_2024_07_24_00_25_model_2.cif
Chain information for fold_2024_07_24_00_25_model_2.cif #12
---
Chain | Description
A | .
Drag select of 32 residues, 96 shapes
> view matrix models
> #12,0.69695,0.32707,0.63819,-0.2953,-0.33387,0.93559,-0.11487,0.33428,-0.63465,-0.13301,0.76126,0.66869
> view matrix models
> #12,0.10781,0.86006,0.49867,-2.2096,-0.71839,0.41412,-0.55894,2.0636,-0.68724,-0.29798,0.66251,1.2261
> view matrix models
> #12,0.64603,0.75453,-0.11547,-3.178,-0.50811,0.31219,-0.80272,1.926,-0.56963,0.57725,0.58507,-2.548
> view matrix models
> #12,-0.55559,0.62681,-0.54628,-2.3602,-0.76886,-0.63741,0.050586,7.2393,-0.3165,0.44812,0.83607,-1.8432
> view matrix models
> #12,0.21649,0.81791,0.53307,-2.4099,-0.95681,0.28626,-0.050645,3.4188,-0.19402,-0.49908,0.84456,1.9451
> open
> /Users/lingxiaobin/Desktop/fold_2024_07_24_00_25/fold_2024_07_24_00_25_model_3.cif
Chain information for fold_2024_07_24_00_25_model_3.cif #16
---
Chain | Description
A | .
> open
> /Users/lingxiaobin/Desktop/fold_2024_07_24_00_25/fold_2024_07_24_00_25_model_4.cif
Chain information for fold_2024_07_24_00_25_model_4.cif #18
---
Chain | Description
A | .
> close #16
> close #12
Drag select of 32 residues, 96 shapes
> view matrix models
> #18,0.19153,-0.83287,0.51928,-2.624,0.15678,0.54824,0.82149,-2.0268,-0.96888,-0.07593,0.23558,0.66834
> view matrix models
> #18,0.2973,-0.6457,-0.70334,0.3794,-0.4858,-0.73646,0.47077,-2.8571,-0.82196,0.20172,-0.53263,2.7578
> view matrix models
> #18,0.54254,0.59936,-0.58857,1.3027,0.45992,-0.79825,-0.38894,0.00744,-0.70294,-0.059683,-0.70874,3.082
> view matrix models
> #18,0.086637,0.2479,-0.9649,1.419,0.29578,-0.93127,-0.2127,-0.65793,-0.95132,-0.26698,-0.15401,1.4216
> view matrix models
> #18,0.22266,-0.39847,-0.88974,0.90714,0.093364,-0.89975,0.42631,-2.2826,-0.97042,-0.17799,-0.16313,1.489
> ui mousemode right "translate selected models"
> view matrix models
> #18,0.22266,-0.39847,-0.88974,8.6984,0.093364,-0.89975,0.42631,208.04,-0.97042,-0.17799,-0.16313,282.85
> view matrix models
> #18,0.22266,-0.39847,-0.88974,123.35,0.093364,-0.89975,0.42631,362.12,-0.97042,-0.17799,-0.16313,250.3
> view matrix models
> #18,0.22266,-0.39847,-0.88974,177.87,0.093364,-0.89975,0.42631,219.42,-0.97042,-0.17799,-0.16313,318.76
> view matrix models
> #18,0.22266,-0.39847,-0.88974,183.56,0.093364,-0.89975,0.42631,216.49,-0.97042,-0.17799,-0.16313,320.1
> view matrix models
> #18,0.22266,-0.39847,-0.88974,187.2,0.093364,-0.89975,0.42631,224.53,-0.97042,-0.17799,-0.16313,295.89
> close #4
> ui mousemode right "rotate selected models"
> view matrix models
> #18,-0.68063,0.063552,-0.72987,186.26,-0.33196,-0.91485,0.2299,224.53,-0.65311,0.39876,0.64377,294.83
> view matrix models
> #18,0.0015937,0.16631,-0.98607,187.62,-0.10894,-0.98018,-0.16549,225.6,-0.99405,0.10769,0.016556,295.68
> view matrix models
> #18,0.0055269,0.31732,-0.9483,187.65,-0.094621,-0.9439,-0.31639,225.98,-0.9955,0.091478,0.024808,295.64
> view matrix models
> #18,-0.046118,-0.94733,-0.31693,185.23,-0.54821,-0.24122,0.8008,223.52,-0.83507,0.21068,-0.50821,297.1
> view matrix models
> #18,-0.048035,-0.94144,-0.33374,185.27,-0.55013,-0.25395,0.79553,223.52,-0.8337,0.22181,-0.50571,297.1
> fitmap #18 inMap #1
Fit molecule fold_2024_07_24_00_25_model_4.cif (#18) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 686 atoms
average map value = 2.942, steps = 112
shifted from previous position = 10.4
rotated from previous position = 14.8 degrees
atoms outside contour = 436, contour level = 4.3314
Position of fold_2024_07_24_00_25_model_4.cif (#18) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.06590966 -0.98997621 -0.12491206 193.67599294
-0.47614337 -0.14121599 0.86795479 230.16636108
-0.87689418 0.00226944 -0.48067811 294.88224782
Axis -0.68893944 0.59845086 0.40892422
Axis point 0.00000000 261.72760072 165.06148681
Rotation angle (degrees) 141.07711070
Shift along axis 124.89671741
> view matrix models
> #18,0.077019,-0.90267,-0.42339,194.43,-0.52123,-0.39846,0.75469,230.18,-0.84994,0.16256,-0.50118,295.08
> ui mousemode right "translate selected models"
> view matrix models
> #18,0.077019,-0.90267,-0.42339,197.97,-0.52123,-0.39846,0.75469,222.77,-0.84994,0.16256,-0.50118,295.77
> view matrix models
> #18,0.077019,-0.90267,-0.42339,196.41,-0.52123,-0.39846,0.75469,223.91,-0.84994,0.16256,-0.50118,290.12
> view matrix models
> #18,0.077019,-0.90267,-0.42339,196.07,-0.52123,-0.39846,0.75469,223.64,-0.84994,0.16256,-0.50118,289.21
> fitmap #18 inMap #1
Fit molecule fold_2024_07_24_00_25_model_4.cif (#18) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 686 atoms
average map value = 2.942, steps = 112
shifted from previous position = 8.86
rotated from previous position = 18.4 degrees
atoms outside contour = 435, contour level = 4.3314
Position of fold_2024_07_24_00_25_model_4.cif (#18) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.06568559 -0.99004984 -0.12444565 193.67458940
-0.47608945 -0.14069951 0.86806824 230.18158493
-0.87694027 0.00222769 -0.48059422 294.89293282
Axis -0.68880760 0.59863680 0.40887415
Axis point 0.00000000 261.81582582 165.05624875
Rotation angle (degrees) 141.05995571
Shift along axis 124.96473355
> ui mousemode right "rotate selected models"
> view matrix models
> #18,-0.38422,-0.038921,0.92242,191.56,-0.20263,0.9783,-0.043125,233.35,-0.90073,-0.20348,-0.38377,294.5
> view matrix models
> #18,-0.35969,-0.64687,0.67244,191.7,-0.59326,0.7148,0.37028,231.82,-0.72018,-0.26575,-0.64087,295.22
> ui mousemode right "translate selected models"
> view matrix models
> #18,-0.35969,-0.64687,0.67244,197.56,-0.59326,0.7148,0.37028,224.21,-0.72018,-0.26575,-0.64087,293.52
> view matrix models
> #18,-0.35969,-0.64687,0.67244,196.79,-0.59326,0.7148,0.37028,224.48,-0.72018,-0.26575,-0.64087,291.59
> fitmap #18 inMap #1
Fit molecule fold_2024_07_24_00_25_model_4.cif (#18) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 686 atoms
average map value = 3.921, steps = 288
shifted from previous position = 10.3
rotated from previous position = 60.2 degrees
atoms outside contour = 335, contour level = 4.3314
Position of fold_2024_07_24_00_25_model_4.cif (#18) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.32534744 -0.94046864 0.09832480 194.26005785
-0.84207764 -0.24085563 0.48259071 227.55564541
-0.43017936 -0.23980677 -0.87030938 300.58032129
Axis -0.80224030 0.58691696 0.10926564
Axis point 0.00000000 229.22619339 130.70399356
Rotation angle (degrees) 153.24107126
Shift along axis 10.55612124
> hide #10 models
> show #10 models
> close #10
> close #3
> hide #9 models
> show #9 models
> hide #!13 models
> show #!13 models
> hide #18 models
> show #18 models
> close #18
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/fold_r_efa/fold_r_efa_model_0.cif
Chain information for fold_r_efa_model_0.cif #3
---
Chain | Description
A | .
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/fold_r_efa/fold_r_efa_model_1.cif
Chain information for fold_r_efa_model_1.cif #4
---
Chain | Description
A | .
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/fold_r_efa/fold_r_efa_model_2.cif
Chain information for fold_r_efa_model_2.cif #10
---
Chain | Description
A | .
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/fold_r_efa/fold_r_efa_model_3.cif
Chain information for fold_r_efa_model_3.cif #12
---
Chain | Description
A | .
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/fold_r_efa/fold_r_efa_model_4.cif
Chain information for fold_r_efa_model_4.cif #16
---
Chain | Description
A | .
> hide #!1 models
> hide #9 models
> hide #11 models
> hide #!13 models
> hide #16 models
> show #16 models
> hide #!5 models
> hide #4 models
> hide #10 models
> hide #12 models
> hide #16 models
> show #4 models
> hide #3 models
> show #10 models
> hide #4 models
> show #12 models
> hide #10 models
> show #16 models
> hide #12 models
> show #3 models
> hide #16 models
> show #!2 models
Drag select of 557 residues, 1132 shapes
> view matrix models #3,1,0,0,65.018,0,1,0,160.49,0,0,1,234.44
> view matrix models #3,1,0,0,230.22,0,1,0,192.13,0,0,1,195.09
> view matrix models #3,1,0,0,236.41,0,1,0,192.96,0,0,1,185.69
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.62922,0.39093,-0.67175,247.93,-0.55279,-0.83266,0.03321,196.62,-0.54636,0.39223,0.74003,189.7
> view matrix models
> #3,-0.73893,-0.40646,0.53737,249.43,0.2991,-0.91254,-0.27896,190.06,0.60376,-0.045403,0.79587,181.17
> view matrix models
> #3,-0.99573,0.019019,-0.090294,250.94,0.0083144,-0.95606,-0.29306,192.18,-0.091899,-0.29256,0.95182,186.32
> view matrix models
> #3,-0.68381,0.43888,-0.58291,248.4,-0.64461,-0.73767,0.2008,197.37,-0.34187,0.51306,0.78733,188.25
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.68381,0.43888,-0.58291,216.17,-0.64461,-0.73767,0.2008,202.13,-0.34187,0.51306,0.78733,222.24
> view matrix models
> #3,-0.68381,0.43888,-0.58291,233.7,-0.64461,-0.73767,0.2008,212.84,-0.34187,0.51306,0.78733,232.9
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.68701,0.29626,-0.66351,233.64,-0.6394,-0.68028,0.3583,212.91,-0.34522,0.67041,0.6568,232.87
> fitmap #3 inMap #2
Fit molecule fold_r_efa_model_0.cif (#3) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 12448 atoms
average map value = 1.143, steps = 224
shifted from previous position = 7.03
rotated from previous position = 22.2 degrees
atoms outside contour = 11320, contour level = 5.0597
Position of fold_r_efa_model_0.cif (#3) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
0.84092403 0.12518636 -0.52647427 208.31410004
-0.54071805 0.15536987 -0.82673103 200.38070814
-0.02169721 0.97989213 0.19834478 205.96625638
Axis 0.90761986 -0.25359228 -0.33454020
Axis point 0.00000000 -9.90081168 273.76511535
Rotation angle (degrees) 84.41517318
Shift along axis 69.35102232
> view matrix models
> #3,-0.78233,0.016003,-0.62266,227.49,-0.16956,-0.96739,0.18817,213.1,-0.59934,0.25279,0.75953,231.4
> view matrix models
> #3,-0.77615,0.014315,-0.63038,227.44,-0.16956,-0.96765,0.1868,213.1,-0.60732,0.25187,0.75348,231.46
> view matrix models
> #3,-0.70248,-0.41757,-0.57633,226.83,0.4769,-0.87728,0.054332,208.28,-0.52829,-0.23669,0.81541,230.8
> view matrix models
> #3,-0.85116,-0.12706,-0.50929,228.17,-0.24415,-0.76308,0.59842,213.97,-0.46467,0.63369,0.61848,230.41
> view matrix models
> #3,-0.95945,-0.021005,-0.28108,229.04,-0.085086,-0.92912,0.35987,212.66,-0.26872,0.36919,0.88966,229.08
> fitmap #3 inMap #2
Fit molecule fold_r_efa_model_0.cif (#3) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 12448 atoms
average map value = 1.049, steps = 184
shifted from previous position = 14.9
rotated from previous position = 4.22 degrees
atoms outside contour = 11372, contour level = 5.0597
Position of fold_r_efa_model_0.cif (#3) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
0.52370262 0.19262791 -0.82983737 201.35997544
-0.85119632 0.07870269 -0.51891301 192.94466134
-0.03464670 0.97811062 0.20518097 200.36413152
Axis 0.75200007 -0.39944823 -0.52434436
Axis point 0.00000000 38.70756236 279.46309514
Rotation angle (degrees) 95.52078611
Shift along axis -30.70849016
> fitmap #3 inMap #2
Fit molecule fold_r_efa_model_0.cif (#3) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 12448 atoms
average map value = 1.049, steps = 48
shifted from previous position = 0.0194
rotated from previous position = 0.0136 degrees
atoms outside contour = 11366, contour level = 5.0597
Position of fold_r_efa_model_0.cif (#3) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
0.52376157 0.19244757 -0.82984200 201.34761426
-0.85115898 0.07857644 -0.51899339 192.93495539
-0.03467298 0.97815627 0.20495880 200.35299278
Axis 0.75207396 -0.39944297 -0.52424238
Axis point 0.00000000 38.71385244 279.40911869
Rotation angle (degrees) 95.52911720
Shift along axis -30.67174585
> close #4
> close #10
> close #12
> close #11,14#13,15
> close #17,19
> close #6-9
> close #25-26
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/fold_r_efa/fold_r_efa_model_0.cif
Chain information for fold_r_efa_model_0.cif #4
---
Chain | Description
A | .
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/fold_r_efa/fold_r_efa_model_0.cif
Chain information for fold_r_efa_model_0.cif #6
---
Chain | Description
A | .
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/fold_r_efa/fold_r_efa_model_0.cif
Chain information for fold_r_efa_model_0.cif #7
---
Chain | Description
A | .
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/fold_r_efa/fold_r_efa_model_0.cif
Chain information for fold_r_efa_model_0.cif #8
---
Chain | Description
A | .
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/fold_r_efa/fold_r_efa_model_0.cif
Chain information for fold_r_efa_model_0.cif #9
---
Chain | Description
A | .
> hide #!2 models
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A #16/A #4/A #6/A #7/A #8/A #9/A
Alignment identifier is 1
> select #3/A:1
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #3/A:2
45 atoms, 49 bonds, 2 residues, 1 model selected
> select add #3/A:3
65 atoms, 70 bonds, 3 residues, 1 model selected
> select add #3/A:4
85 atoms, 91 bonds, 4 residues, 1 model selected
> select add #3/A:5
108 atoms, 116 bonds, 5 residues, 1 model selected
> select add #3/A:6
130 atoms, 140 bonds, 6 residues, 1 model selected
> select up
12448 atoms, 13961 bonds, 580 residues, 1 model selected
> hide sel target a
> select clear
> select #3/A:1
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #3/A:2
45 atoms, 49 bonds, 2 residues, 1 model selected
> select add #3/A:3
65 atoms, 70 bonds, 3 residues, 1 model selected
> select add #3/A:4
85 atoms, 91 bonds, 4 residues, 1 model selected
> select #3/A:5
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #3/A:6
22 atoms, 24 bonds, 1 residue, 1 model selected
> select clear
> select #3/A:1
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #3/A:2
45 atoms, 49 bonds, 2 residues, 1 model selected
> select add #3/A:3
65 atoms, 70 bonds, 3 residues, 1 model selected
> select add #3/A:4
85 atoms, 91 bonds, 4 residues, 1 model selected
> select add #3/A:5
108 atoms, 116 bonds, 5 residues, 1 model selected
> select add #3/A:6
130 atoms, 140 bonds, 6 residues, 1 model selected
> select add #3/A:7
152 atoms, 164 bonds, 7 residues, 1 model selected
> select add #3/A:8
174 atoms, 188 bonds, 8 residues, 1 model selected
> select add #3/A:9
196 atoms, 212 bonds, 9 residues, 1 model selected
> select add #3/A:10
218 atoms, 236 bonds, 10 residues, 1 model selected
> select add #3/A:12
238 atoms, 257 bonds, 11 residues, 1 model selected
> select add #3/A:11
258 atoms, 278 bonds, 12 residues, 1 model selected
> select add #3/A:573
278 atoms, 299 bonds, 13 residues, 1 model selected
> select add #3/A:574
298 atoms, 320 bonds, 14 residues, 1 model selected
> select add #3/A:575
318 atoms, 341 bonds, 15 residues, 1 model selected
> select add #3/A:576
338 atoms, 362 bonds, 16 residues, 1 model selected
> select add #3/A:577
358 atoms, 383 bonds, 17 residues, 1 model selected
> select add #3/A:578
381 atoms, 408 bonds, 18 residues, 1 model selected
> select add #3/A:580
404 atoms, 433 bonds, 19 residues, 1 model selected
> select add #3/A:579
426 atoms, 457 bonds, 20 residues, 1 model selected
> select add #3/A:572
448 atoms, 481 bonds, 21 residues, 1 model selected
> select add #3/A:571
471 atoms, 506 bonds, 22 residues, 1 model selected
> select add #3/A:570
491 atoms, 527 bonds, 23 residues, 1 model selected
> select add #3/A:569
511 atoms, 548 bonds, 24 residues, 1 model selected
> select add #3/A:568
534 atoms, 573 bonds, 25 residues, 1 model selected
> select add #3/A:567
554 atoms, 594 bonds, 26 residues, 1 model selected
> select add #3/A:566
574 atoms, 615 bonds, 27 residues, 1 model selected
> select add #3/A:13
596 atoms, 639 bonds, 28 residues, 1 model selected
> select add #3/A:14
618 atoms, 663 bonds, 29 residues, 1 model selected
> select add #3/A:15
638 atoms, 684 bonds, 30 residues, 1 model selected
> select add #3/A:16
660 atoms, 708 bonds, 31 residues, 1 model selected
> select add #3/A:17
683 atoms, 733 bonds, 32 residues, 1 model selected
> select add #3/A:18
705 atoms, 757 bonds, 33 residues, 1 model selected
> select add #3/A:19
725 atoms, 778 bonds, 34 residues, 1 model selected
> select add #3/A:20
745 atoms, 799 bonds, 35 residues, 1 model selected
> select add #3/A:21
765 atoms, 820 bonds, 36 residues, 1 model selected
> select add #3/A:565
785 atoms, 841 bonds, 37 residues, 1 model selected
> select add #3/A:564
807 atoms, 865 bonds, 38 residues, 1 model selected
> select add #3/A:563
829 atoms, 889 bonds, 39 residues, 1 model selected
> select add #3/A:561
849 atoms, 910 bonds, 40 residues, 1 model selected
> select add #3/A:562
871 atoms, 934 bonds, 41 residues, 1 model selected
> select add #3/A:560
891 atoms, 955 bonds, 42 residues, 1 model selected
> select add #3/A:168
911 atoms, 976 bonds, 43 residues, 1 model selected
> select subtract #3/A:168
891 atoms, 955 bonds, 42 residues, 1 model selected
> select add #3/A:559
911 atoms, 976 bonds, 43 residues, 1 model selected
> select add #3/A:558
934 atoms, 1001 bonds, 44 residues, 1 model selected
> select add #3/A:557
956 atoms, 1025 bonds, 45 residues, 1 model selected
> select add #3/A:556
978 atoms, 1049 bonds, 46 residues, 1 model selected
> select add #3/A:555
1000 atoms, 1073 bonds, 47 residues, 1 model selected
> select add #3/A:554
1022 atoms, 1097 bonds, 48 residues, 1 model selected
> select add #3/A:553
1045 atoms, 1122 bonds, 49 residues, 1 model selected
> select add #3/A:552
1067 atoms, 1146 bonds, 50 residues, 1 model selected
> select add #3/A:551
1089 atoms, 1170 bonds, 51 residues, 1 model selected
> select add #3/A:550
1112 atoms, 1195 bonds, 52 residues, 1 model selected
> select add #3/A:549
1135 atoms, 1220 bonds, 53 residues, 1 model selected
> select add #3/A:22
1157 atoms, 1244 bonds, 54 residues, 1 model selected
> select add #3/A:23
1179 atoms, 1268 bonds, 55 residues, 1 model selected
> select add #3/A:24
1201 atoms, 1292 bonds, 56 residues, 1 model selected
> select add #3/A:548
1223 atoms, 1316 bonds, 57 residues, 1 model selected
> select add #3/A:547
1243 atoms, 1337 bonds, 58 residues, 1 model selected
> select add #3/A:546
1266 atoms, 1362 bonds, 59 residues, 1 model selected
> select add #3/A:545
1288 atoms, 1386 bonds, 60 residues, 1 model selected
> select add #3/A:544
1310 atoms, 1410 bonds, 61 residues, 1 model selected
> select add #3/A:543
1333 atoms, 1435 bonds, 62 residues, 1 model selected
> select add #3/A:25
1353 atoms, 1456 bonds, 63 residues, 1 model selected
> select add #3/A:26
1373 atoms, 1477 bonds, 64 residues, 1 model selected
> select add #3/A:27
1393 atoms, 1498 bonds, 65 residues, 1 model selected
> select add #3/A:28
1415 atoms, 1522 bonds, 66 residues, 1 model selected
> select add #3/A:29
1438 atoms, 1547 bonds, 67 residues, 1 model selected
> select add #3/A:30
1458 atoms, 1568 bonds, 68 residues, 1 model selected
> select add #3/A:31
1481 atoms, 1593 bonds, 69 residues, 1 model selected
> select add #3/A:32
1503 atoms, 1617 bonds, 70 residues, 1 model selected
> select add #3/A:33
1525 atoms, 1641 bonds, 71 residues, 1 model selected
> select add #3/A:34
1548 atoms, 1666 bonds, 72 residues, 1 model selected
> select add #3/A:35
1570 atoms, 1690 bonds, 73 residues, 1 model selected
> select add #3/A:36
1593 atoms, 1715 bonds, 74 residues, 1 model selected
> select add #3/A:37
1613 atoms, 1736 bonds, 75 residues, 1 model selected
> select add #3/A:38
1635 atoms, 1760 bonds, 76 residues, 1 model selected
> select add #3/A:39
1655 atoms, 1781 bonds, 77 residues, 1 model selected
> select add #3/A:40
1675 atoms, 1802 bonds, 78 residues, 1 model selected
> select add #3/A:41
1695 atoms, 1823 bonds, 79 residues, 1 model selected
> select add #3/A:42
1718 atoms, 1848 bonds, 80 residues, 1 model selected
> select add #3/A:43
1740 atoms, 1872 bonds, 81 residues, 1 model selected
> select add #3/A:44
1762 atoms, 1896 bonds, 82 residues, 1 model selected
> select add #3/A:45
1782 atoms, 1917 bonds, 83 residues, 1 model selected
> select add #3/A:46
1804 atoms, 1941 bonds, 84 residues, 1 model selected
> select add #3/A:47
1826 atoms, 1965 bonds, 85 residues, 1 model selected
> select add #3/A:48
1846 atoms, 1986 bonds, 86 residues, 1 model selected
> select add #3/A:49
1869 atoms, 2011 bonds, 87 residues, 1 model selected
> select add #3/A:51
1892 atoms, 2036 bonds, 88 residues, 1 model selected
> select add #3/A:52
1912 atoms, 2057 bonds, 89 residues, 1 model selected
> select add #3/A:50
1932 atoms, 2078 bonds, 90 residues, 1 model selected
> select add #3/A:53
1952 atoms, 2099 bonds, 91 residues, 1 model selected
> select add #3/A:54
1974 atoms, 2123 bonds, 92 residues, 1 model selected
> select add #3/A:55
1997 atoms, 2148 bonds, 93 residues, 1 model selected
> select add #3/A:56
2020 atoms, 2173 bonds, 94 residues, 1 model selected
> select add #3/A:57
2043 atoms, 2198 bonds, 95 residues, 1 model selected
> select add #3/A:58
2063 atoms, 2219 bonds, 96 residues, 1 model selected
> select add #3/A:59
2085 atoms, 2243 bonds, 97 residues, 1 model selected
> select add #3/A:60
2108 atoms, 2268 bonds, 98 residues, 1 model selected
> select ~sel & ##selected
10340 atoms, 11597 bonds, 482 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!2 models
> volume #2 level 2.228
> select #3/A:1
23 atoms, 25 bonds, 1 residue, 1 model selected
> view matrix models
> #3,-0.09423,0.57381,0.81355,293.53,-0.81519,-0.51356,0.26781,241.31,0.57148,-0.63796,0.51616,170.92
> view matrix models
> #3,0.020321,0.38575,0.92238,287.64,-0.94044,-0.30576,0.14859,247.86,0.33935,-0.87046,0.35656,151.45
> view matrix models
> #3,0.15044,0.78627,0.59929,298.65,-0.98163,0.046848,0.18495,268.26,0.11735,-0.61611,0.77887,179.38
> fitmap #3 inMap #2
Fit molecule fold_r_efa_model_0.cif (#3) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 2108 atoms
average map value = 2.819, steps = 164
shifted from previous position = 2.06
rotated from previous position = 17.1 degrees
atoms outside contour = 1222, contour level = 2.2281
Position of fold_r_efa_model_0.cif (#3) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
0.38812494 -0.01043207 -0.92154772 189.19124918
0.37243799 0.91642365 0.14648430 271.14245758
0.84299999 -0.40007359 0.35957218 134.45930536
Axis -0.28971809 -0.93534720 0.20295084
Axis point -91.97257033 0.00000000 177.97975063
Rotation angle (degrees) 70.60611984
Shift along axis -281.13583682
> volume #2 style surface
> select #3/A:23
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #3/A:24
44 atoms, 48 bonds, 2 residues, 1 model selected
> select add #3/A:25
64 atoms, 69 bonds, 3 residues, 1 model selected
> select add #3/A:26
84 atoms, 90 bonds, 4 residues, 1 model selected
> select add #3/A:27
104 atoms, 111 bonds, 5 residues, 1 model selected
> select add #3/A:28
126 atoms, 135 bonds, 6 residues, 1 model selected
> select add #3/A:30
146 atoms, 156 bonds, 7 residues, 1 model selected
> select add #3/A:29
169 atoms, 181 bonds, 8 residues, 1 model selected
> select add #3/A:31
192 atoms, 206 bonds, 9 residues, 1 model selected
> select add #3/A:32
214 atoms, 230 bonds, 10 residues, 1 model selected
> select add #3/A:33
236 atoms, 254 bonds, 11 residues, 1 model selected
> select add #3/A:34
259 atoms, 279 bonds, 12 residues, 1 model selected
> select add #3/A:35
281 atoms, 303 bonds, 13 residues, 1 model selected
> select add #3/A:36
304 atoms, 328 bonds, 14 residues, 1 model selected
> select add #3/A:37
324 atoms, 349 bonds, 15 residues, 1 model selected
> select add #3/A:38
346 atoms, 373 bonds, 16 residues, 1 model selected
> select add #3/A:39
366 atoms, 394 bonds, 17 residues, 1 model selected
> select add #3/A:40
386 atoms, 415 bonds, 18 residues, 1 model selected
> select add #3/A:41
406 atoms, 436 bonds, 19 residues, 1 model selected
> select add #3/A:42
429 atoms, 461 bonds, 20 residues, 1 model selected
> select add #3/A:43
451 atoms, 485 bonds, 21 residues, 1 model selected
> select add #3/A:44
473 atoms, 509 bonds, 22 residues, 1 model selected
> select add #3/A:45
493 atoms, 530 bonds, 23 residues, 1 model selected
> select add #3/A:46
515 atoms, 554 bonds, 24 residues, 1 model selected
> select add #3/A:47
537 atoms, 578 bonds, 25 residues, 1 model selected
> select add #3/A:48
557 atoms, 599 bonds, 26 residues, 1 model selected
> select add #3/A:50
577 atoms, 620 bonds, 27 residues, 1 model selected
> select add #3/A:49
600 atoms, 645 bonds, 28 residues, 1 model selected
> select add #3/A:51
623 atoms, 670 bonds, 29 residues, 1 model selected
> select add #3/A:52
643 atoms, 691 bonds, 30 residues, 1 model selected
> select add #3/A:53
663 atoms, 712 bonds, 31 residues, 1 model selected
> select add #3/A:54
685 atoms, 736 bonds, 32 residues, 1 model selected
> select add #3/A:55
708 atoms, 761 bonds, 33 residues, 1 model selected
> select add #3/A:56
731 atoms, 786 bonds, 34 residues, 1 model selected
> select add #3/A:57
754 atoms, 811 bonds, 35 residues, 1 model selected
> select add #3/A:58
774 atoms, 832 bonds, 36 residues, 1 model selected
> select add #3/A:59
796 atoms, 856 bonds, 37 residues, 1 model selected
> select add #3/A:60
819 atoms, 881 bonds, 38 residues, 1 model selected
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-loop2.pdb models #3
> selectedOnly true relModel #3
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-loop2.pdb
Chain information for R-loop2.pdb #10
---
Chain | Description
A | No description available
> hide #10 models
> show #10 models
> delete atoms sel
> delete bonds sel
> select clear
> select #4/A:43
22 atoms, 24 bonds, 1 residue, 1 model selected
> view matrix models
> #4,1,-0.0029769,0.00051301,-0.00050014,0.0029699,0.99991,0.013134,0.00060934,-0.00055207,-0.013132,0.99991,-0.0023182
> hide #7 models
> hide #8 models
> hide #9 models
> hide #6 models
> hide #4 models
Drag select of 38 residues, 114 shapes
> ui mousemode right "translate selected models"
> view matrix models #10,1,0,0,260.11,0,1,0,268.38,0,0,1,239.63
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.30271,0.51513,0.80188,290.25,-0.9355,0.32145,0.14664,212.21,-0.18223,-0.79455,0.57921,181.97
> view matrix models
> #10,-0.54403,-0.36943,0.75336,220.36,-0.81064,-0.00029981,-0.58554,184.92,0.21654,-0.92926,-0.29931,169.05
> view matrix models
> #10,-0.69654,0.58398,0.41689,271.96,-0.69333,-0.3982,-0.60061,162.28,-0.18474,-0.70739,0.68226,188.64
> view matrix models
> #10,-0.66321,0.65194,0.36759,276.07,-0.74786,-0.55816,-0.35939,154.67,-0.029134,-0.51326,0.85774,205.62
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.66321,0.65194,0.36759,247.98,-0.74786,-0.55816,-0.35939,216.08,-0.029134,-0.51326,0.85774,194.46
> view matrix models
> #10,-0.66321,0.65194,0.36759,251.55,-0.74786,-0.55816,-0.35939,221.71,-0.029134,-0.51326,0.85774,193.61
> view matrix models
> #10,-0.66321,0.65194,0.36759,264.11,-0.74786,-0.55816,-0.35939,236.77,-0.029134,-0.51326,0.85774,172.57
> view matrix models
> #10,-0.66321,0.65194,0.36759,278.65,-0.74786,-0.55816,-0.35939,221.09,-0.029134,-0.51326,0.85774,177.13
> view matrix models
> #10,-0.66321,0.65194,0.36759,279.8,-0.74786,-0.55816,-0.35939,225.46,-0.029134,-0.51326,0.85774,178.54
> fitmap #10 inMap #2
Fit molecule R-loop2.pdb (#10) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 819 atoms
average map value = 2.879, steps = 116
shifted from previous position = 8.11
rotated from previous position = 21.4 degrees
atoms outside contour = 482, contour level = 2.2281
Position of R-loop2.pdb (#10) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
0.31392893 0.47144851 -0.82412677 212.87585752
-0.52901542 0.80763924 0.26050249 264.17195273
0.78841063 0.35419650 0.50294485 185.35811970
Axis 0.04931275 -0.84870583 -0.52656116
Axis point 96.66929260 0.00000000 196.45686807
Rotation angle (degrees) 71.80472899
Shift along axis -311.30917066
> show #4 models
> hide #!3 models
> show #!3 models
> select clear
> select up
12448 atoms, 13961 bonds, 580 residues, 1 model selected
> hide sel target a
> select clear
> select #4/A:60
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #4/A:175
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add #4/A:174
66 atoms, 71 bonds, 3 residues, 1 model selected
> select add #4/A:173
86 atoms, 92 bonds, 4 residues, 1 model selected
> select add #4/A:172
108 atoms, 116 bonds, 5 residues, 1 model selected
> select add #4/A:171
128 atoms, 137 bonds, 6 residues, 1 model selected
> select add #4/A:169
150 atoms, 161 bonds, 7 residues, 1 model selected
> select add #4/A:170
170 atoms, 182 bonds, 8 residues, 1 model selected
> select add #4/A:61
190 atoms, 203 bonds, 9 residues, 1 model selected
> select add #4/A:62
212 atoms, 227 bonds, 10 residues, 1 model selected
> select add #4/A:140
232 atoms, 248 bonds, 11 residues, 1 model selected
> select subtract #4/A:140
212 atoms, 227 bonds, 10 residues, 1 model selected
> select add #4/A:63
232 atoms, 248 bonds, 11 residues, 1 model selected
> select add #4/A:64
255 atoms, 273 bonds, 12 residues, 1 model selected
> select add #4/A:65
278 atoms, 298 bonds, 13 residues, 1 model selected
> select add #4/A:168
298 atoms, 319 bonds, 14 residues, 1 model selected
> select add #4/A:167
321 atoms, 344 bonds, 15 residues, 1 model selected
> select add #4/A:166
343 atoms, 368 bonds, 16 residues, 1 model selected
> select add #4/A:66
366 atoms, 393 bonds, 17 residues, 1 model selected
> select add #4/A:67
388 atoms, 417 bonds, 18 residues, 1 model selected
> select add #4/A:68
408 atoms, 438 bonds, 19 residues, 1 model selected
> select add #4/A:69
430 atoms, 462 bonds, 20 residues, 1 model selected
> select add #4/A:70
452 atoms, 486 bonds, 21 residues, 1 model selected
> select add #4/A:434
472 atoms, 507 bonds, 22 residues, 1 model selected
> select subtract #4/A:434
452 atoms, 486 bonds, 21 residues, 1 model selected
> select add #4/A:71
475 atoms, 511 bonds, 22 residues, 1 model selected
> select add #4/A:165
497 atoms, 535 bonds, 23 residues, 1 model selected
> select add #4/A:164
519 atoms, 559 bonds, 24 residues, 1 model selected
> select add #4/A:163
539 atoms, 580 bonds, 25 residues, 1 model selected
> select add #4/A:72
559 atoms, 601 bonds, 26 residues, 1 model selected
> select add #4/A:73
579 atoms, 622 bonds, 27 residues, 1 model selected
> select add #4/A:74
602 atoms, 647 bonds, 28 residues, 1 model selected
> select add #4/A:75
624 atoms, 671 bonds, 29 residues, 1 model selected
> select add #4/A:76
644 atoms, 692 bonds, 30 residues, 1 model selected
> select add #4/A:77
666 atoms, 716 bonds, 31 residues, 1 model selected
> select add #4/A:79
686 atoms, 737 bonds, 32 residues, 1 model selected
> select add #4/A:78
708 atoms, 761 bonds, 33 residues, 1 model selected
> select add #4/A:80
728 atoms, 782 bonds, 34 residues, 1 model selected
> select add #4/A:81
750 atoms, 806 bonds, 35 residues, 1 model selected
> select add #4/A:82
772 atoms, 830 bonds, 36 residues, 1 model selected
> select add #4/A:83
794 atoms, 854 bonds, 37 residues, 1 model selected
> select add #4/A:84
816 atoms, 878 bonds, 38 residues, 1 model selected
> select add #4/A:85
836 atoms, 899 bonds, 39 residues, 1 model selected
> select add #4/A:86
859 atoms, 924 bonds, 40 residues, 1 model selected
> select add #4/A:87
881 atoms, 948 bonds, 41 residues, 1 model selected
> select add #4/A:88
903 atoms, 972 bonds, 42 residues, 1 model selected
> select add #4/A:89
923 atoms, 993 bonds, 43 residues, 1 model selected
> select add #4/A:90
943 atoms, 1014 bonds, 44 residues, 1 model selected
> select add #4/A:91
966 atoms, 1039 bonds, 45 residues, 1 model selected
> select add #4/A:92
989 atoms, 1064 bonds, 46 residues, 1 model selected
> select add #4/A:93
1012 atoms, 1089 bonds, 47 residues, 1 model selected
> select add #4/A:94
1034 atoms, 1113 bonds, 48 residues, 1 model selected
> select add #4/A:95
1054 atoms, 1134 bonds, 49 residues, 1 model selected
> select add #4/A:96
1076 atoms, 1158 bonds, 50 residues, 1 model selected
> select add #4/A:97
1096 atoms, 1179 bonds, 51 residues, 1 model selected
> select add #4/A:98
1116 atoms, 1200 bonds, 52 residues, 1 model selected
> select add #4/A:99
1139 atoms, 1225 bonds, 53 residues, 1 model selected
Drag select of 6 residues
> select add #4/A:175
155 atoms, 21 bonds, 7 residues, 1 model selected
> select add #4/A:174
178 atoms, 46 bonds, 8 residues, 1 model selected
> select add #4/A:173
198 atoms, 67 bonds, 9 residues, 1 model selected
> select add #4/A:172
220 atoms, 91 bonds, 10 residues, 1 model selected
> select add #4/A:171
240 atoms, 112 bonds, 11 residues, 1 model selected
> select add #4/A:170
260 atoms, 133 bonds, 12 residues, 1 model selected
> select add #4/A:169
282 atoms, 157 bonds, 13 residues, 1 model selected
> color #4 #ec3acaff
> select add #4/A:60
305 atoms, 182 bonds, 14 residues, 1 model selected
> select add #4/A:61
325 atoms, 203 bonds, 15 residues, 1 model selected
> select add #4/A:62
347 atoms, 227 bonds, 16 residues, 1 model selected
> select add #4/A:63
367 atoms, 248 bonds, 17 residues, 1 model selected
> select add #4/A:64
390 atoms, 273 bonds, 18 residues, 1 model selected
> select add #4/A:167
413 atoms, 298 bonds, 19 residues, 1 model selected
> select add #4/A:168
433 atoms, 319 bonds, 20 residues, 1 model selected
> select add #4/A:166
455 atoms, 343 bonds, 21 residues, 1 model selected
> select add #4/A:165
477 atoms, 367 bonds, 22 residues, 1 model selected
> select add #4/A:164
499 atoms, 391 bonds, 23 residues, 1 model selected
> select add #4/A:65
522 atoms, 416 bonds, 24 residues, 1 model selected
> select add #4/A:66
545 atoms, 441 bonds, 25 residues, 1 model selected
> select add #4/A:67
567 atoms, 465 bonds, 26 residues, 1 model selected
> select add #4/A:68
587 atoms, 486 bonds, 27 residues, 1 model selected
> select add #4/A:69
609 atoms, 510 bonds, 28 residues, 1 model selected
> select add #4/A:70
631 atoms, 534 bonds, 29 residues, 1 model selected
> select add #4/A:71
654 atoms, 559 bonds, 30 residues, 1 model selected
> select add #4/A:72
674 atoms, 580 bonds, 31 residues, 1 model selected
> select add #4/A:73
694 atoms, 601 bonds, 32 residues, 1 model selected
> select add #4/A:74
717 atoms, 626 bonds, 33 residues, 1 model selected
> select add #4/A:75
739 atoms, 650 bonds, 34 residues, 1 model selected
> select add #4/A:163
759 atoms, 671 bonds, 35 residues, 1 model selected
> select add #4/A:162
782 atoms, 696 bonds, 36 residues, 1 model selected
> select add #4/A:161
802 atoms, 717 bonds, 37 residues, 1 model selected
> select add #4/A:160
822 atoms, 738 bonds, 38 residues, 1 model selected
> select add #4/A:159
844 atoms, 762 bonds, 39 residues, 1 model selected
> select add #4/A:158
866 atoms, 786 bonds, 40 residues, 1 model selected
> select add #4/A:157
886 atoms, 807 bonds, 41 residues, 1 model selected
> select add #4/A:76
906 atoms, 828 bonds, 42 residues, 1 model selected
> select add #4/A:77
928 atoms, 852 bonds, 43 residues, 1 model selected
> select add #4/A:78
950 atoms, 876 bonds, 44 residues, 1 model selected
> select add #4/A:79
970 atoms, 897 bonds, 45 residues, 1 model selected
> select subtract #4/A:216
948 atoms, 897 bonds, 44 residues, 1 model selected
> select subtract #4/A:215
925 atoms, 897 bonds, 43 residues, 1 model selected
> select add #4/A:88
947 atoms, 921 bonds, 44 residues, 1 model selected
> select add #4/A:89
967 atoms, 942 bonds, 45 residues, 1 model selected
> select add #4/A:90
987 atoms, 963 bonds, 46 residues, 1 model selected
> select add #4/A:91
1010 atoms, 988 bonds, 47 residues, 1 model selected
> select add #4/A:92
1033 atoms, 1013 bonds, 48 residues, 1 model selected
> select add #4/A:93
1056 atoms, 1038 bonds, 49 residues, 1 model selected
> select add #4/A:94
1078 atoms, 1062 bonds, 50 residues, 1 model selected
> select add #4/A:95
1098 atoms, 1083 bonds, 51 residues, 1 model selected
> select add #4/A:96
1120 atoms, 1107 bonds, 52 residues, 1 model selected
> select add #4/A:97
1140 atoms, 1128 bonds, 53 residues, 1 model selected
> select add #4/A:98
1160 atoms, 1149 bonds, 54 residues, 1 model selected
> select add #4/A:101
1180 atoms, 1170 bonds, 55 residues, 1 model selected
> select add #4/A:102
1200 atoms, 1191 bonds, 56 residues, 1 model selected
> select add #4/A:103
1223 atoms, 1216 bonds, 57 residues, 1 model selected
> select add #4/A:104
1245 atoms, 1240 bonds, 58 residues, 1 model selected
> select add #4/A:105
1265 atoms, 1261 bonds, 59 residues, 1 model selected
> select add #4/A:106
1285 atoms, 1282 bonds, 60 residues, 1 model selected
> select add #4/A:107
1305 atoms, 1303 bonds, 61 residues, 1 model selected
> select add #4/A:108
1325 atoms, 1324 bonds, 62 residues, 1 model selected
> select add #4/A:85
1345 atoms, 1345 bonds, 63 residues, 1 model selected
> select add #4/A:84
1367 atoms, 1369 bonds, 64 residues, 1 model selected
> select add #4/A:83
1389 atoms, 1393 bonds, 65 residues, 1 model selected
> select add #4/A:81
1411 atoms, 1417 bonds, 66 residues, 1 model selected
> select add #4/A:82
1433 atoms, 1441 bonds, 67 residues, 1 model selected
> select add #4/A:80
1453 atoms, 1462 bonds, 68 residues, 1 model selected
> select add #4/A:109
1475 atoms, 1486 bonds, 69 residues, 1 model selected
> select add #4/A:110
1498 atoms, 1511 bonds, 70 residues, 1 model selected
> select add #4/A:111
1518 atoms, 1532 bonds, 71 residues, 1 model selected
> select add #4/A:112
1541 atoms, 1557 bonds, 72 residues, 1 model selected
> select add #4/A:113
1564 atoms, 1582 bonds, 73 residues, 1 model selected
> select add #4/A:114
1584 atoms, 1603 bonds, 74 residues, 1 model selected
> select add #4/A:115
1607 atoms, 1628 bonds, 75 residues, 1 model selected
> select add #4/A:116
1630 atoms, 1653 bonds, 76 residues, 1 model selected
> select add #4/A:117
1652 atoms, 1677 bonds, 77 residues, 1 model selected
> select add #4/A:118
1672 atoms, 1698 bonds, 78 residues, 1 model selected
> select add #4/A:119
1692 atoms, 1719 bonds, 79 residues, 1 model selected
> select add #4/A:120
1712 atoms, 1740 bonds, 80 residues, 1 model selected
> select add #4/A:121
1732 atoms, 1761 bonds, 81 residues, 1 model selected
> select add #4/A:122
1754 atoms, 1785 bonds, 82 residues, 1 model selected
> select add #4/A:123
1774 atoms, 1806 bonds, 83 residues, 1 model selected
> select add #4/A:124
1796 atoms, 1830 bonds, 84 residues, 1 model selected
> select add #4/A:125
1819 atoms, 1855 bonds, 85 residues, 1 model selected
> select add #4/A:126
1839 atoms, 1876 bonds, 86 residues, 1 model selected
> select add #4/A:127
1861 atoms, 1900 bonds, 87 residues, 1 model selected
> select add #4/A:128
1883 atoms, 1924 bonds, 88 residues, 1 model selected
> select add #4/A:129
1903 atoms, 1945 bonds, 89 residues, 1 model selected
> select add #4/A:130
1926 atoms, 1970 bonds, 90 residues, 1 model selected
> select add #4/A:131
1946 atoms, 1991 bonds, 91 residues, 1 model selected
> select add #4/A:132
1968 atoms, 2015 bonds, 92 residues, 1 model selected
> select add #4/A:133
1990 atoms, 2039 bonds, 93 residues, 1 model selected
> select add #4/A:134
2012 atoms, 2063 bonds, 94 residues, 1 model selected
> select add #4/A:135
2034 atoms, 2087 bonds, 95 residues, 1 model selected
> select add #4/A:136
2056 atoms, 2111 bonds, 96 residues, 1 model selected
> select add #4/A:137
2079 atoms, 2136 bonds, 97 residues, 1 model selected
> select add #4/A:138
2102 atoms, 2161 bonds, 98 residues, 1 model selected
> select add #4/A:139
2124 atoms, 2185 bonds, 99 residues, 1 model selected
> select add #4/A:140
2144 atoms, 2206 bonds, 100 residues, 1 model selected
> select add #4/A:141
2164 atoms, 2227 bonds, 101 residues, 1 model selected
> select add #4/A:142
2186 atoms, 2251 bonds, 102 residues, 1 model selected
> select add #4/A:143
2208 atoms, 2275 bonds, 103 residues, 1 model selected
> select add #4/A:144
2228 atoms, 2296 bonds, 104 residues, 1 model selected
> select add #4/A:156
2248 atoms, 2317 bonds, 105 residues, 1 model selected
> select add #4/A:155
2270 atoms, 2341 bonds, 106 residues, 1 model selected
> select add #4/A:154
2290 atoms, 2362 bonds, 107 residues, 1 model selected
> select add #4/A:153
2310 atoms, 2383 bonds, 108 residues, 1 model selected
> select add #4/A:145
2332 atoms, 2407 bonds, 109 residues, 1 model selected
> select add #4/A:146
2355 atoms, 2432 bonds, 110 residues, 1 model selected
> select add #4/A:152
2378 atoms, 2457 bonds, 111 residues, 1 model selected
> select add #4/A:151
2400 atoms, 2481 bonds, 112 residues, 1 model selected
> select add #4/A:150
2422 atoms, 2505 bonds, 113 residues, 1 model selected
> select add #4/A:149
2444 atoms, 2529 bonds, 114 residues, 1 model selected
> select add #4/A:148
2466 atoms, 2553 bonds, 115 residues, 1 model selected
> select add #4/A:147
2486 atoms, 2574 bonds, 116 residues, 1 model selected
> select ~sel & ##selected
9962 atoms, 11174 bonds, 464 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 64 residues
> view matrix models
> #4,1,-0.0029769,0.00051301,22.527,0.0029699,0.99991,0.013134,12.645,-0.00055207,-0.013132,0.99991,127.1
> view matrix models
> #4,1,-0.0029769,0.00051301,39.626,0.0029699,0.99991,0.013134,43.979,-0.00055207,-0.013132,0.99991,289.28
> view matrix models
> #4,1,-0.0029769,0.00051301,245.91,0.0029699,0.99991,0.013134,189.72,-0.00055207,-0.013132,0.99991,239.65
> view matrix models
> #4,1,-0.0029769,0.00051301,263.99,0.0029699,0.99991,0.013134,226.5,-0.00055207,-0.013132,0.99991,241.24
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.83124,-0.11286,0.54434,276.32,-0.48111,-0.63663,0.60269,226.58,0.27852,-0.76287,-0.58349,195.98
> view matrix models
> #4,0.72328,-0.35124,-0.59456,241.83,-0.61456,-0.72007,-0.32221,198.7,-0.31495,0.59844,-0.73667,192.94
> view matrix models
> #4,0.90778,-0.41455,0.063925,262.01,-0.27254,-0.69879,-0.66138,193.64,0.31884,0.58296,-0.74733,200.4
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.90778,-0.41455,0.063925,229.4,-0.27254,-0.69879,-0.66138,206.54,0.31884,0.58296,-0.74733,215.69
> view matrix models
> #4,0.90778,-0.41455,0.063925,220.87,-0.27254,-0.69879,-0.66138,213.08,0.31884,0.58296,-0.74733,209.85
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.63387,-0.61638,0.46721,227.41,-0.015471,-0.61405,-0.78912,213.25,0.77328,0.49297,-0.39877,224.6
> view matrix models
> #4,0.6497,-0.61703,0.44403,226.96,-0.0059338,-0.5882,-0.80869,212.98,0.76016,0.52278,-0.38582,224.99
> fitmap #4 inMap #2
Fit molecule fold_r_efa_model_0.cif (#4) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 2486 atoms
average map value = 3.215, steps = 112
shifted from previous position = 3.7
rotated from previous position = 13.8 degrees
atoms outside contour = 1275, contour level = 2.2281
Position of fold_r_efa_model_0.cif (#4) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
-0.69776293 -0.17111572 0.69559063 215.43515823
0.60135688 -0.66755966 0.43901482 197.58637483
0.38922591 0.72462647 0.56869999 201.98460624
Axis 0.32503180 0.34864921 0.87908934
Axis point 58.89163084 73.55827418 0.00000000
Rotation angle (degrees) 153.93697465
Shift along axis 316.47412339
> select clear
> select #4/A:73
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #4/A:72
40 atoms, 42 bonds, 2 residues, 1 model selected
> select add #4/A:71
63 atoms, 67 bonds, 3 residues, 1 model selected
> select add #4/A:70
85 atoms, 91 bonds, 4 residues, 1 model selected
> select add #4/A:69
107 atoms, 115 bonds, 5 residues, 1 model selected
> select add #4/A:68
127 atoms, 136 bonds, 6 residues, 1 model selected
> select add #4/A:67
149 atoms, 160 bonds, 7 residues, 1 model selected
> select add #4/A:66
172 atoms, 185 bonds, 8 residues, 1 model selected
> select add #4/A:65
195 atoms, 210 bonds, 9 residues, 1 model selected
> select add #4/A:64
218 atoms, 235 bonds, 10 residues, 1 model selected
> select add #4/A:63
238 atoms, 256 bonds, 11 residues, 1 model selected
> select add #4/A:62
260 atoms, 280 bonds, 12 residues, 1 model selected
> select add #4/A:61
280 atoms, 301 bonds, 13 residues, 1 model selected
> select add #4/A:60
303 atoms, 326 bonds, 14 residues, 1 model selected
> select add #4/A:165
325 atoms, 350 bonds, 15 residues, 1 model selected
> select add #4/A:166
347 atoms, 374 bonds, 16 residues, 1 model selected
> select add #4/A:167
370 atoms, 399 bonds, 17 residues, 1 model selected
> select add #4/A:168
390 atoms, 420 bonds, 18 residues, 1 model selected
> select add #4/A:169
412 atoms, 444 bonds, 19 residues, 1 model selected
> select add #4/A:170
432 atoms, 465 bonds, 20 residues, 1 model selected
> select add #4/A:171
452 atoms, 486 bonds, 21 residues, 1 model selected
> select add #4/A:172
474 atoms, 510 bonds, 22 residues, 1 model selected
> select add #4/A:173
494 atoms, 531 bonds, 23 residues, 1 model selected
> select add #4/A:174
517 atoms, 556 bonds, 24 residues, 1 model selected
> select add #4/A:175
537 atoms, 577 bonds, 25 residues, 1 model selected
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R4-1.pdb models #4
> selectedOnly true relModel #4
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R4-1.pdb
Chain information for R4-1.pdb #11
---
Chain | Description
A | No description available
> delete atoms sel
> delete bonds sel
Drag select of 25 residues, 1 pseudobonds, 75 shapes
> ui mousemode right "translate selected models"
> view matrix models #11,1,0,0,270.78,0,1,0,359.22,0,0,1,204.09
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models #11,1,0,0,222.67,0,1,0,343.42,0,0,1,202.23
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.20215,0.89821,-0.39034,229.08,-0.7443,-0.39994,-0.53484,268.66,-0.63651,0.18241,0.74939,193.82
> view matrix models
> #11,0.34426,0.58651,0.73314,258.03,-0.48503,0.7797,-0.396,318.01,-0.80389,-0.21926,0.55289,171.61
> view matrix models
> #11,-0.74749,-0.13217,0.65099,217.17,0.66048,-0.043327,0.74959,336.3,-0.070866,0.99028,0.11968,210.38
> view matrix models
> #11,0.069951,-0.78264,0.61854,202.46,0.88268,-0.24031,-0.40388,297.21,0.46473,0.57422,0.67401,218.38
> view matrix models
> #11,0.23328,-0.84628,0.47895,197.89,0.73389,-0.16991,-0.65767,290.37,0.63795,0.50492,0.58144,215.14
> view matrix models
> #11,0.23612,-0.78358,0.57468,203.04,0.58097,-0.36022,-0.72987,279.62,0.77892,0.50621,0.37018,210.48
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.23612,-0.78358,0.57468,213.66,0.58097,-0.36022,-0.72987,248.7,0.77892,0.50621,0.37018,257.36
> view matrix models
> #11,0.23612,-0.78358,0.57468,218.32,0.58097,-0.36022,-0.72987,241.4,0.77892,0.50621,0.37018,253.82
> view matrix models
> #11,0.23612,-0.78358,0.57468,212.44,0.58097,-0.36022,-0.72987,242.99,0.77892,0.50621,0.37018,255.47
> fitmap #11 inMap #2
Fit molecule R4-1.pdb (#11) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 537 atoms
average map value = 5.219, steps = 128
shifted from previous position = 12.3
rotated from previous position = 26.3 degrees
atoms outside contour = 145, contour level = 2.2281
Position of R4-1.pdb (#11) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
-0.93449672 0.32657079 0.14165943 206.24932565
-0.12459596 -0.67285215 0.72920904 185.95633779
0.33345423 0.66379326 0.66946754 206.09696691
Axis -0.13226354 -0.38778809 -0.91220982
Axis point 93.31271687 37.58954309 0.00000000
Rotation angle (degrees) 165.68259869
Shift along axis -287.39459639
> view matrix models
> #11,0.11475,-0.71758,0.68696,216.31,0.23654,-0.6519,-0.72047,219.21,0.96482,0.24517,0.094928,235.54
> view matrix models
> #11,0.11475,-0.71758,0.68696,216.69,0.23654,-0.6519,-0.72047,220.6,0.96482,0.24517,0.094928,234.54
> view matrix models
> #11,0.11475,-0.71758,0.68696,217.45,0.23654,-0.6519,-0.72047,221.37,0.96482,0.24517,0.094928,233.68
> view matrix models
> #11,0.11475,-0.71758,0.68696,217.75,0.23654,-0.6519,-0.72047,222.07,0.96482,0.24517,0.094928,236.35
> view matrix models
> #11,0.11475,-0.71758,0.68696,218.07,0.23654,-0.6519,-0.72047,222.65,0.96482,0.24517,0.094928,237.71
> view matrix models
> #11,0.11475,-0.71758,0.68696,216.67,0.23654,-0.6519,-0.72047,221.05,0.96482,0.24517,0.094928,239.52
> view matrix models
> #11,0.11475,-0.71758,0.68696,218.36,0.23654,-0.6519,-0.72047,221.43,0.96482,0.24517,0.094928,237.42
> fitmap #11 inMap #2
Fit molecule R4-1.pdb (#11) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 537 atoms
average map value = 5.999, steps = 148
shifted from previous position = 5.31
rotated from previous position = 29.5 degrees
atoms outside contour = 101, contour level = 2.2281
Position of R4-1.pdb (#11) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
-0.68570177 0.45758134 0.56606749 228.64509932
0.02347268 -0.76338525 0.64551685 183.34736074
0.72750403 0.45591917 0.51271395 196.21949788
Axis -0.37884747 -0.32257686 -0.86742076
Axis point 77.43998217 47.20491052 0.00000000
Rotation angle (degrees) 165.50890228
Shift along axis -315.97009746
> volume #2 level 4.199
> hide #!3 models
> hide #4 models
> hide #10 models
> hide #!11 models
> show #!5 models
> open /Users/lingxiaobin/Desktop/Wangzefeng_Cte/PIE_C_3dot75_emready.mrc
Opened PIE_C_3dot75_emready.mrc as #12, grid size 256,256,256, pixel 1.2,
shown at level 0.275, step 1, values float32
> hide #!1 models
> hide #!5 models
> volume #12 level 3.238
> volume #12 level 0.33
> volume #12 level 0.8238
> volume #12 level 4.061
> volume #12 level 0.9335
> volume #12 level 3.841
> volume #12 level 1.043
> volume #12 level 0.714
> volume #12 level 0.4946
> volume #12 level 2.854
> volume #12 level 4.664
> volume #12 level 1.811
> volume #12 level 0.4946
> volume #12 level 2.415
> volume #12 level 3.951
> show #!12 models
> close #12
> show #16 models
> show #!2 models
> hide #16 models
> show #!3 models
> show #4 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #!5 models
> hide #!5 models
> show #7 models
> hide #7 models
> show #!11 models
> hide #!11 models
> combine #3 #4
Remapping chain ID 'A' in fold_r_efa_model_0.cif #4 to 'B'
> hide #!3 models
> hide #4 models
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-3-4.pdb models #12 relModel
> #2
> open
> /Users/lingxiaobin/Desktop/ROOL:GOLLD/RealSpaceRefine_11/R-3-4_real_space_refined_011.pdb
Chain information for R-3-4_real_space_refined_011.pdb #13
---
Chain | Description
A | No description available
B | No description available
> hide #!12 models
> select #13/B:161
20 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.45542,0.51435,0.72666,110.9,-0.65849,0.3547,-0.66377,389.25,-0.59915,-0.78079,0.17716,429.23
> view matrix models
> #13,-0.92997,0.24533,0.27381,349.41,-0.16242,0.39399,-0.90465,309.45,-0.32981,-0.88577,-0.32655,474.49
> view matrix models
> #13,-0.5206,0.55746,0.64669,131.59,-0.39237,0.51649,-0.7611,314.12,-0.7583,-0.64998,-0.050153,480.2
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.5206,0.55746,0.64669,111.57,-0.39237,0.51649,-0.7611,327.45,-0.7583,-0.64998,-0.050153,472.27
> view matrix models
> #13,-0.5206,0.55746,0.64669,143.86,-0.39237,0.51649,-0.7611,325.29,-0.7583,-0.64998,-0.050153,505.51
> view matrix models
> #13,-0.5206,0.55746,0.64669,146.03,-0.39237,0.51649,-0.7611,326.96,-0.7583,-0.64998,-0.050153,509.91
> fitmap #13 inMap #2
Fit molecule R-3-4_real_space_refined_011.pdb (#13) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 3238 atoms
average map value = 2.5, steps = 196
shifted from previous position = 4.41
rotated from previous position = 31.1 degrees
atoms outside contour = 2384, contour level = 4.1986
Position of R-3-4_real_space_refined_011.pdb (#13) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
0.96950016 -0.20384917 -0.13606967 69.33246269
0.22627539 0.53113340 0.81651501 -62.72682417
-0.09417476 -0.82240065 0.56105997 280.15473278
Axis -0.96694860 -0.02471770 0.25377044
Axis point 0.00000000 228.10348775 207.63659916
Rotation angle (degrees) 57.93731454
Shift along axis 5.60452375
> hide #!2 models
Drag select of 93 residues, 183 shapes
> select subtract #13/A:548
1969 atoms, 92 residues, 1 model selected
> select subtract #13/A:547
1949 atoms, 91 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!2 models
> show #!3 models
> hide #!3 models
> show #4 models
> select #4/A:90
20 atoms, 21 bonds, 1 residue, 1 model selected
> fitmap #4 inMap #2
Fit molecule fold_r_efa_model_0.cif (#4) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 1949 atoms
average map value = 3.614, steps = 172
shifted from previous position = 1.66
rotated from previous position = 7.92 degrees
atoms outside contour = 1160, contour level = 4.1986
Position of fold_r_efa_model_0.cif (#4) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
-0.63396826 -0.27036787 0.72455880 218.05882018
0.65404760 -0.68739276 0.31577355 195.26763343
0.41268145 0.67408635 0.61261865 204.30543347
Axis 0.34475481 0.30007640 0.88943705
Axis point 53.58634244 80.38726561 0.00000000
Rotation angle (degrees) 148.69033522
Shift along axis 315.48885966
> select up
1949 atoms, 2185 bonds, 91 residues, 1 model selected
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-3.pdb models #4
> selectedOnly true relModel #2
> open
> /Users/lingxiaobin/Desktop/ROOL:GOLLD/RealSpaceRefine_12/R-3_real_space_refined_012.pdb
Chain information for R-3_real_space_refined_012.pdb #14
---
Chain | Description
A | No description available
> select subtract #4
Nothing selected
> hide #4 models
> select clear
> select #14/A:108
20 atoms, 21 bonds, 1 residue, 1 model selected
> view matrix models #14,1,0,0,-23.288,0,1,0,45.891,0,0,1,4.1028
> view matrix models #14,1,0,0,6.2042,0,1,0,46.424,0,0,1,23.548
> view matrix models #14,1,0,0,-3.2075,0,1,0,57.224,0,0,1,33.282
> view matrix models #14,1,0,0,-3.4578,0,1,0,62.668,0,0,1,34.749
> ui mousemode right "rotate selected models"
> view matrix models
> #14,-0.34995,0.93457,0.06413,117.4,-0.015603,0.062634,-0.99791,405.04,-0.93664,-0.35023,-0.007337,477.57
> view matrix models
> #14,-0.59771,0.71836,-0.35595,283.29,0.51716,0.0062123,-0.85587,273.99,-0.61261,-0.69564,-0.37522,532.53
> view matrix models
> #14,-0.91451,0.25039,-0.31776,425.02,0.10706,-0.60767,-0.78694,455.61,-0.39013,-0.75368,0.52892,332.51
> view matrix models
> #14,-0.55071,0.64137,-0.53419,318.12,0.21444,-0.50978,-0.83315,423.89,-0.80668,-0.57338,0.14321,460.77
> ui mousemode right "translate selected models"
> view matrix models
> #14,-0.55071,0.64137,-0.53419,305.28,0.21444,-0.50978,-0.83315,433.22,-0.80668,-0.57338,0.14321,467.84
> view matrix models
> #14,-0.55071,0.64137,-0.53419,309.46,0.21444,-0.50978,-0.83315,433.35,-0.80668,-0.57338,0.14321,469.85
> fitmap #14 inMap #2
Fit molecule R-3_real_space_refined_012.pdb (#14) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 1949 atoms
average map value = 5.341, steps = 212
shifted from previous position = 6.01
rotated from previous position = 51.5 degrees
atoms outside contour = 776, contour level = 4.1986
Position of R-3_real_space_refined_012.pdb (#14) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
0.99999057 0.00136313 0.00412220 -1.00478763
-0.00136129 0.99999897 -0.00045123 0.43435028
-0.00412281 0.00044562 0.99999140 0.79798120
Axis 0.10273580 0.94448211 -0.31208796
Axis point 197.42870392 0.00000000 245.64675523
Rotation angle (degrees) 0.25008693
Shift along axis 0.05796810
> close #14
> open
> /Users/lingxiaobin/Desktop/ROOL:GOLLD/RealSpaceRefine_13/R-3_real_space_refined_013.pdb
Chain information for R-3_real_space_refined_013.pdb #14
---
Chain | Description
A | No description available
> select #14/A:110
23 atoms, 25 bonds, 1 residue, 1 model selected
> view matrix models #14,1,0,0,-21.922,0,1,0,29.113,0,0,1,1.4382
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.25235,0.88037,0.40158,-82.534,-0.31276,0.46695,-0.82713,335.96,-0.9157,0.083131,0.39318,293.87
> view matrix models
> #14,-0.045143,0.99342,0.10523,15.485,0.23036,0.11285,-0.96654,303.76,-0.97206,-0.019393,-0.23394,435.56
> ui mousemode right "translate selected models"
> view matrix models
> #14,-0.045143,0.99342,0.10523,0.72319,0.23036,0.11285,-0.96654,338.22,-0.97206,-0.019393,-0.23394,439.55
> view matrix models
> #14,-0.045143,0.99342,0.10523,17.201,0.23036,0.11285,-0.96654,327.35,-0.97206,-0.019393,-0.23394,456.37
> fitmap #14 inMap #2
Fit molecule R-3_real_space_refined_013.pdb (#14) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 1949 atoms
average map value = 2.87, steps = 164
shifted from previous position = 17.1
rotated from previous position = 25.2 degrees
atoms outside contour = 1332, contour level = 4.1986
Position of R-3_real_space_refined_013.pdb (#14) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
0.89735394 -0.08425762 0.43319344 -38.04997430
0.09595783 0.99537196 -0.00517197 -19.75290368
-0.43075283 0.04620940 0.90128613 102.70040802
Axis 0.05812131 0.97727426 0.20385519
Axis point 207.32573338 0.00000000 136.88448686
Rotation angle (degrees) 26.23272970
Shift along axis -0.57950790
> close #14
> show #4 models
> hide #!2 models
> select #4/A:123
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #4/A:122
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add #4/A:121
62 atoms, 66 bonds, 3 residues, 1 model selected
> select add #4/A:120
82 atoms, 87 bonds, 4 residues, 1 model selected
> select add #4/A:124
104 atoms, 111 bonds, 5 residues, 1 model selected
> select add #4/A:125
127 atoms, 136 bonds, 6 residues, 1 model selected
> select add #4/A:126
147 atoms, 157 bonds, 7 residues, 1 model selected
> select add #4/A:127
169 atoms, 181 bonds, 8 residues, 1 model selected
> select add #4/A:128
191 atoms, 205 bonds, 9 residues, 1 model selected
> select add #4/A:129
211 atoms, 226 bonds, 10 residues, 1 model selected
> select add #4/A:130
234 atoms, 251 bonds, 11 residues, 1 model selected
> select add #4/A:131
254 atoms, 272 bonds, 12 residues, 1 model selected
> select add #4/A:132
276 atoms, 296 bonds, 13 residues, 1 model selected
> select add #4/A:133
298 atoms, 320 bonds, 14 residues, 1 model selected
> select add #4/A:135
320 atoms, 344 bonds, 15 residues, 1 model selected
> select add #4/A:136
342 atoms, 368 bonds, 16 residues, 1 model selected
> select add #4/A:116
365 atoms, 393 bonds, 17 residues, 1 model selected
> select add #4/A:117
387 atoms, 417 bonds, 18 residues, 1 model selected
> select add #4/A:118
407 atoms, 438 bonds, 19 residues, 1 model selected
> select add #4/A:119
427 atoms, 459 bonds, 20 residues, 1 model selected
> select add #4/A:134
449 atoms, 483 bonds, 21 residues, 1 model selected
> select add #4/A:115
472 atoms, 508 bonds, 22 residues, 1 model selected
> select add #4/A:114
492 atoms, 529 bonds, 23 residues, 1 model selected
> select add #4/A:113
515 atoms, 554 bonds, 24 residues, 1 model selected
> select add #4/A:137
538 atoms, 579 bonds, 25 residues, 1 model selected
> select add #4/A:138
561 atoms, 604 bonds, 26 residues, 1 model selected
> select add #4/A:139
583 atoms, 628 bonds, 27 residues, 1 model selected
> select add #4/A:140
603 atoms, 649 bonds, 28 residues, 1 model selected
> select add #4/A:142
625 atoms, 673 bonds, 29 residues, 1 model selected
> select add #4/A:143
647 atoms, 697 bonds, 30 residues, 1 model selected
> select add #4/A:141
667 atoms, 718 bonds, 31 residues, 1 model selected
> select add #4/A:159
689 atoms, 742 bonds, 32 residues, 1 model selected
> select add #4/A:158
711 atoms, 766 bonds, 33 residues, 1 model selected
> select add #4/A:157
731 atoms, 787 bonds, 34 residues, 1 model selected
> select add #4/A:156
751 atoms, 808 bonds, 35 residues, 1 model selected
> select add #4/A:155
773 atoms, 832 bonds, 36 residues, 1 model selected
> select add #4/A:154
793 atoms, 853 bonds, 37 residues, 1 model selected
> select add #4/A:153
813 atoms, 874 bonds, 38 residues, 1 model selected
> select add #4/A:151
835 atoms, 898 bonds, 39 residues, 1 model selected
> select add #4/A:152
858 atoms, 923 bonds, 40 residues, 1 model selected
> select add #4/A:150
880 atoms, 947 bonds, 41 residues, 1 model selected
> select add #4/A:149
902 atoms, 971 bonds, 42 residues, 1 model selected
> select add #4/A:148
924 atoms, 995 bonds, 43 residues, 1 model selected
> select add #4/A:147
944 atoms, 1016 bonds, 44 residues, 1 model selected
> select add #4/A:146
967 atoms, 1041 bonds, 45 residues, 1 model selected
> select add #4/A:145
989 atoms, 1065 bonds, 46 residues, 1 model selected
> select add #4/A:144
1009 atoms, 1086 bonds, 47 residues, 1 model selected
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R5.pdb models #4 relModel #4
> hide #!13 models
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R5.pdb models #4 selectedOnly
> true relModel #4
> open
> /Users/lingxiaobin/Desktop/ROOL:GOLLD/RealSpaceRefine_15/R5_real_space_refined_015.pdb
Chain information for R5_real_space_refined_015.pdb #14
---
Chain | Description
A | No description available
> show #!2 models
> delete atoms sel
> delete bonds sel
> select #14/A:114
20 atoms, 21 bonds, 1 residue, 1 model selected
> view matrix models #14,1,0,0,-22.765,0,1,0,14.023,0,0,1,3.9193
> view matrix models #14,1,0,0,-0.91925,0,1,0,18.967,0,0,1,38.006
> view matrix models #14,1,0,0,4.4032,0,1,0,35.818,0,0,1,35.26
> fitmap #14 inMap #2
Fit molecule R5_real_space_refined_015.pdb (#14) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 1009 atoms
average map value = 2.657, steps = 124
shifted from previous position = 8.87
rotated from previous position = 19.5 degrees
atoms outside contour = 738, contour level = 4.1986
Position of R5_real_space_refined_015.pdb (#14) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
-0.52336932 -0.58098848 -0.62332731 550.88887068
0.85064176 -0.31336887 -0.42214755 139.72796728
0.04993149 -0.75116732 0.65822072 201.41188634
Axis -0.20361536 -0.41664922 0.88597078
Axis point 257.53700948 275.74666620 0.00000000
Rotation angle (degrees) 126.10442372
Shift along axis 8.05806364
> view matrix models
> #14,0.95359,-0.17829,-0.24263,85.68,0.13992,0.97594,-0.16723,51.564,0.26661,0.12553,0.9556,-42.044
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.77597,0.43596,-0.45586,42.497,-0.60229,0.29739,-0.74081,446.35,-0.18739,0.84941,0.49334,-2.4433
> view matrix models
> #14,0.25527,0.9477,0.19159,-56.137,-0.66384,0.31586,-0.6779,445.25,-0.70296,0.045861,0.70975,228.84
> view matrix models
> #14,0.034362,0.99933,0.01279,13.482,-0.47909,0.027702,-0.87733,495.72,-0.87709,0.024019,0.47972,311.51
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.034362,0.99933,0.01279,19.546,-0.47909,0.027702,-0.87733,490.86,-0.87709,0.024019,0.47972,310.97
> fitmap #14 inMap #2
Fit molecule R5_real_space_refined_015.pdb (#14) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 1009 atoms
average map value = 6.982, steps = 124
shifted from previous position = 5.69
rotated from previous position = 16.7 degrees
atoms outside contour = 306, contour level = 4.1986
Position of R5_real_space_refined_015.pdb (#14) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
0.99999814 -0.00191877 0.00019583 0.29587457
0.00191919 0.99999579 -0.00217526 -0.01311031
-0.00019165 0.00217563 0.99999762 -0.37717802
Axis 0.74826206 0.06663871 0.66004785
Axis point 0.00000000 164.73131517 -5.47446407
Rotation angle (degrees) 0.16657814
Shift along axis -0.02843748
> select clear
> select #14/A:136
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #14/A:118
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add #14/A:135
64 atoms, 69 bonds, 3 residues, 1 model selected
> select add #14/A:134
86 atoms, 93 bonds, 4 residues, 1 model selected
> select add #14/A:133
108 atoms, 117 bonds, 5 residues, 1 model selected
> select add #14/A:132
130 atoms, 141 bonds, 6 residues, 1 model selected
> select add #14/A:131
150 atoms, 162 bonds, 7 residues, 1 model selected
> select add #14/A:130
173 atoms, 187 bonds, 8 residues, 1 model selected
> select add #14/A:129
193 atoms, 208 bonds, 9 residues, 1 model selected
> select add #14/A:128
215 atoms, 232 bonds, 10 residues, 1 model selected
> select add #14/A:127
237 atoms, 256 bonds, 11 residues, 1 model selected
> select add #14/A:126
257 atoms, 277 bonds, 12 residues, 1 model selected
> select add #14/A:125
280 atoms, 302 bonds, 13 residues, 1 model selected
> select add #14/A:124
302 atoms, 326 bonds, 14 residues, 1 model selected
> select add #14/A:123
322 atoms, 347 bonds, 15 residues, 1 model selected
> select add #14/A:122
344 atoms, 371 bonds, 16 residues, 1 model selected
> select add #14/A:121
364 atoms, 392 bonds, 17 residues, 1 model selected
> select add #14/A:120
384 atoms, 413 bonds, 18 residues, 1 model selected
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R6.pdb models #14
> selectedOnly true relModel #14
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R6.pdb
Chain information for R6.pdb #15
---
Chain | Description
A | No description available
> delete atoms sel
> delete bonds sel
> select #15/A:132
22 atoms, 24 bonds, 1 residue, 1 model selected
> view matrix models #15,1,0,0,-32.381,0,1,0,26.552,0,0,1,20.867
> view matrix models #15,1,0,0,3.4378,0,1,0,55.071,0,0,1,22.22
> view matrix models #15,1,0,0,0.20389,0,1,0,50.027,0,0,1,28.038
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.57601,0.78799,-0.21745,-27.604,-0.51831,0.14636,-0.84258,464.47,-0.63211,0.59804,0.49273,128.94
> view matrix models
> #15,0.79428,0.08912,-0.60098,122.09,-0.58579,0.37472,-0.71863,414.89,0.16116,0.92284,0.34984,-87.903
> view matrix models
> #15,0.80365,-0.14811,-0.57637,163.03,-0.43267,0.51956,-0.73679,355.27,0.40858,0.8415,0.35346,-127.01
> ui mousemode right "translate selected models"
> view matrix models
> #15,0.80365,-0.14811,-0.57637,158.46,-0.43267,0.51956,-0.73679,356.91,0.40858,0.8415,0.35346,-122.34
> view matrix models
> #15,0.80365,-0.14811,-0.57637,163.26,-0.43267,0.51956,-0.73679,357.9,0.40858,0.8415,0.35346,-122.52
> view matrix models
> #15,0.80365,-0.14811,-0.57637,161.63,-0.43267,0.51956,-0.73679,355.38,0.40858,0.8415,0.35346,-118.82
> view matrix models
> #15,0.80365,-0.14811,-0.57637,164.91,-0.43267,0.51956,-0.73679,355.54,0.40858,0.8415,0.35346,-117.2
> view matrix models
> #15,0.80365,-0.14811,-0.57637,165.52,-0.43267,0.51956,-0.73679,355.77,0.40858,0.8415,0.35346,-117.45
> view matrix models
> #15,0.80365,-0.14811,-0.57637,166.32,-0.43267,0.51956,-0.73679,356.36,0.40858,0.8415,0.35346,-117.51
> fitmap #15 inMap #2
Fit molecule R6.pdb (#15) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 393 atoms
average map value = 5.937, steps = 96
shifted from previous position = 3.69
rotated from previous position = 18.9 degrees
atoms outside contour = 126, contour level = 4.1986
Position of R6.pdb (#15) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
-0.38477259 -0.92105294 -0.06009602 494.50292538
0.74751637 -0.27275977 -0.60565781 184.68832310
0.54145114 -0.27796328 0.79345263 -29.59609700
Axis 0.18167816 -0.33350565 0.92507677
Axis point 187.19365573 255.27820863 0.00000000
Rotation angle (degrees) 115.59708481
Shift along axis 0.86711923
> show #!5 models
> hide #!5 models
> close #5
> show #!3 models
> show #!13 models
> close #4
> show #6 models
> hide #6 models
> show #!12 models
> hide #!13 models
> hide #!14 models
> hide #!15 models
> hide #!2 models
Drag select of 15 residues
> delete atoms sel
> delete bonds sel
Drag select of 22 residues
> delete atoms sel
> delete bonds sel
Drag select of 6 residues, 1 pseudobonds
> delete atoms (#!12 & sel)
> delete bonds (#!12 & sel)
> select #12/B:158
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #12/B:159
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #12/B:158
44 atoms, 48 bonds, 2 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
Drag select of 2 residues
> select clear
No visible atoms or bonds selected
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> hide #12.1 models
> show #!2 models
> show #!13 models
> show #!14 models
> show #!15 models
> hide #!12 models
> show #!12 models
> hide #!3 models
> show #!3 models
> hide #!12 models
> show #!12 models
> hide #!13 models
> select #3/A:3
20 atoms, 21 bonds, 1 residue, 1 model selected
> hide #!3 models
> select add #3
1289 atoms, 1445 bonds, 1 pseudobond, 60 residues, 2 models selected
> select subtract #3
Nothing selected
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!2 models
Drag select of 39 residues
> delete atoms sel
> delete bonds sel
Drag select of 20 residues
> delete atoms sel
> delete bonds sel
> show #!2 models
> show #!13 models
> hide #!15 models
> show #!15 models
> hide #!13 models
> combine #12 #14 #15
Remapping chain ID 'A' in R5_real_space_refined_015.pdb #14 to 'C'
Remapping chain ID 'A' in R6.pdb #15 to 'D'
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!12 models
> hide #!14 models
> hide #!15 models
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-C.pdb models #4 relModel #4
> open
> /Users/lingxiaobin/Desktop/ROOL:GOLLD/RealSpaceRefine_16/R-C_real_space_refined_016.pdb
Chain information for R-C_real_space_refined_016.pdb #5
---
Chain | Description
B | No description available
C | No description available
D | No description available
> hide #!4 models
> select #5/B:110
23 atoms, 25 bonds, 1 residue, 1 model selected
> view matrix models #5,1,0,0,-24.148,0,1,0,47.24,0,0,1,-1.7121
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.20571,-0.61919,-0.75782,390.12,0.59006,0.69626,-0.40871,46.814,0.78071,-0.36309,0.50859,-17.998
> view matrix models
> #5,-0.90541,0.36883,-0.21025,358.11,0.10382,-0.28784,-0.95204,419.89,-0.41166,-0.88381,0.22232,379.69
> view matrix models
> #5,0.18192,0.93002,0.31933,-67.666,-0.38328,0.36612,-0.84797,391.76,-0.90554,0.031867,0.42306,290
> view matrix models
> #5,0.01387,0.9531,0.30234,-32.619,-0.33791,0.28905,-0.89569,403.99,-0.94108,-0.089742,0.32607,336.14
> view matrix models
> #5,0.31598,0.89916,0.30277,-88.048,-0.7293,0.43431,-0.52868,397.02,-0.60686,-0.05376,0.79299,174.82
> view matrix models
> #5,0.33289,0.91845,0.21362,-79.088,-0.6731,0.3901,-0.6283,410.5,-0.66039,0.065363,0.74807,173.55
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.33289,0.91845,0.21362,-66.03,-0.6731,0.3901,-0.6283,429.35,-0.66039,0.065363,0.74807,204.92
> view matrix models
> #5,0.33289,0.91845,0.21362,-68.292,-0.6731,0.3901,-0.6283,424.14,-0.66039,0.065363,0.74807,208.42
> view matrix models
> #5,0.33289,0.91845,0.21362,-69.591,-0.6731,0.3901,-0.6283,424.18,-0.66039,0.065363,0.74807,208.87
> fitmap #5 inMap #2
Fit molecule R-C_real_space_refined_016.pdb (#5) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 1972 atoms
average map value = 7.189, steps = 160
shifted from previous position = 3.37
rotated from previous position = 37.7 degrees
atoms outside contour = 417, contour level = 4.1986
Position of R-C_real_space_refined_016.pdb (#5) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
0.99999737 0.00203637 -0.00105463 -0.21940479
-0.00203728 0.99999756 -0.00085845 0.57354136
0.00105288 0.00086060 0.99999908 -0.41240431
Axis 0.35096126 -0.43027144 -0.83168063
Axis point 285.44595458 111.42176711 0.00000000
Rotation angle (degrees) 0.14032040
Shift along axis 0.01920763
> close #12
> show #!15 models
> hide #!15 models
> show #!13 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> close #14
> show #!15 models
> hide #!15 models
> close #15
> show #16 models
> hide #16 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #7 models
> hide #7 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #9 models
> hide #9 models
> show #10 models
> hide #10 models
> show #10 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> close #3
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> close #4
> hide #!5 models
> show #!5 models
> show #6 models
> hide #6 models
> hide #10 models
> show #10 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!13 models
> show #!13 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #10 models
> show #10 models
> show #16 models
> hide #16 models
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> combine #5 #10 #11 #13
Remapping chain ID 'A' in R4-1.pdb #11 to 'E'
Remapping chain ID 'A' in R-3-4_real_space_refined_011.pdb #13 to 'F'
> hide #!3 models
> show #!3 models
> hide #!5 models
> hide #10 models
> hide #!11 models
> hide #!13 models
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R7.pdb models #3 relModel #3
> ui tool show "Model Panel"
> show #!5 models
> hide #!3 models
> show #!3 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> select add #5
1972 atoms, 2204 bonds, 3 pseudobonds, 93 residues, 2 models selected
> select subtract #5
Nothing selected
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!5 models
> hide #!3 models
> close #5
> show #6 models
> select #6/A:579
22 atoms, 24 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #16/A #6/A #7/A #8/A #9/A #10/A #11/A #3/A #3/E
Alignment identifier is 1
> select #16/A:1 #6/A:1 #7/A:1 #8/A:1 #9/A:1
115 atoms, 125 bonds, 5 residues, 5 models selected
> select #16/A:1-106 #6/A:1-106 #7/A:1-106 #8/A:1-106 #9/A:1-106 #10/A
> #11/A:60-73 #3/A/E:60-73
13629 atoms, 15284 bonds, 634 residues, 8 models selected
. [ID: 1] region 9 chains [1-106] RMSD: 229.230
> delete atoms (#6 & sel)
> delete bonds (#6 & sel)
> select #16/A:107 #6/A:107 #7/A:107 #8/A:107 #9/A:107
100 atoms, 105 bonds, 5 residues, 5 models selected
> select #16/A:107-157 #6/A:107-157 #7/A:107-157 #8/A:107-157 #9/A:107-157
5465 atoms, 6125 bonds, 255 residues, 5 models selected
. [ID: 1] region 9 chains [107-157] RMSD: 13.326
> delete atoms (#6 & sel)
> delete bonds (#6 & sel)
> select #16/A:158 #6/A:158 #7/A:158 #8/A:158 #9/A:158
110 atoms, 120 bonds, 5 residues, 5 models selected
> select #16/A:158-174 #6/A:158-174 #7/A:158-174 #8/A:158-174 #9/A:158-174
> #11/A:165-174 #3/E:165-174
2243 atoms, 2508 bonds, 105 residues, 7 models selected
. [ID: 1] region 9 chains [158-174] RMSD: 276.080
> delete atoms (#6 & sel)
> delete bonds (#6 & sel)
Drag select of 22 residues, 45 shapes
> delete atoms sel
> delete bonds sel
Drag select of 7 residues, 17 shapes
> delete atoms sel
> delete bonds sel
Drag select of 2 shapes
> delete atoms sel
> delete bonds sel
Drag select of 35 residues, 69 shapes
> select add #6/A:191
777 atoms, 25 bonds, 36 residues, 1 model selected
> select add #6/A:192
797 atoms, 46 bonds, 37 residues, 1 model selected
> select add #6/A:528
819 atoms, 70 bonds, 38 residues, 1 model selected
> select add #6/A:527
841 atoms, 94 bonds, 39 residues, 1 model selected
> select add #6/A:526
861 atoms, 115 bonds, 40 residues, 1 model selected
> select add #6/A:525
883 atoms, 139 bonds, 41 residues, 1 model selected
> select add #6/A:193
905 atoms, 163 bonds, 42 residues, 1 model selected
> select add #6/A:194
927 atoms, 187 bonds, 43 residues, 1 model selected
> select add #6/A:195
950 atoms, 212 bonds, 44 residues, 1 model selected
> select add #6/A:196
973 atoms, 237 bonds, 45 residues, 1 model selected
> select add #6/A:524
995 atoms, 261 bonds, 46 residues, 1 model selected
> select add #6/A:523
1018 atoms, 286 bonds, 47 residues, 1 model selected
> select add #6/A:522
1038 atoms, 307 bonds, 48 residues, 1 model selected
> select add #6/A:520
1080 atoms, 331 bonds, 50 residues, 1 model selected
> select add #6/A:519
1103 atoms, 356 bonds, 51 residues, 1 model selected
> select add #6/A:518
1123 atoms, 377 bonds, 52 residues, 1 model selected
> select add #6/A:517
1146 atoms, 402 bonds, 53 residues, 1 model selected
> select add #6/A:197
1166 atoms, 423 bonds, 54 residues, 1 model selected
> select add #6/A:198
1188 atoms, 447 bonds, 55 residues, 1 model selected
> select add #6/A:346
1210 atoms, 471 bonds, 56 residues, 1 model selected
> select add #6/A:345
1230 atoms, 492 bonds, 57 residues, 1 model selected
> select add #6/A:344
1253 atoms, 517 bonds, 58 residues, 1 model selected
> select add #6/A:343
1276 atoms, 542 bonds, 59 residues, 1 model selected
> select add #6/A:342
1296 atoms, 563 bonds, 60 residues, 1 model selected
> select add #6/A:341
1316 atoms, 584 bonds, 61 residues, 1 model selected
> select add #6/A:340
1339 atoms, 609 bonds, 62 residues, 1 model selected
> select add #6/A:339
1361 atoms, 633 bonds, 63 residues, 1 model selected
> select add #6/A:338
1383 atoms, 657 bonds, 64 residues, 1 model selected
> select add #6/A:337
1406 atoms, 682 bonds, 65 residues, 1 model selected
> select add #6/A:336
1428 atoms, 706 bonds, 66 residues, 1 model selected
> select add #6/A:335
1450 atoms, 730 bonds, 67 residues, 1 model selected
> select add #6/A:203
1472 atoms, 754 bonds, 68 residues, 1 model selected
> select add #6/A:202
1494 atoms, 778 bonds, 69 residues, 1 model selected
> select add #6/A:201
1516 atoms, 802 bonds, 70 residues, 1 model selected
> select add #6/A:200
1539 atoms, 827 bonds, 71 residues, 1 model selected
> select add #6/A:199
1559 atoms, 848 bonds, 72 residues, 1 model selected
> select add #6/A:204
1579 atoms, 869 bonds, 73 residues, 1 model selected
> select add #6/A:205
1599 atoms, 890 bonds, 74 residues, 1 model selected
> select add #6/A:206
1619 atoms, 911 bonds, 75 residues, 1 model selected
> select add #6/A:207
1639 atoms, 932 bonds, 76 residues, 1 model selected
> select add #6/A:208
1659 atoms, 953 bonds, 77 residues, 1 model selected
> select add #6/A:334
1681 atoms, 977 bonds, 78 residues, 1 model selected
> select add #6/A:333
1704 atoms, 1002 bonds, 79 residues, 1 model selected
> select add #6/A:209
1727 atoms, 1027 bonds, 80 residues, 1 model selected
> select add #6/A:210
1749 atoms, 1051 bonds, 81 residues, 1 model selected
> select add #6/A:211
1772 atoms, 1076 bonds, 82 residues, 1 model selected
> select add #6/A:212
1792 atoms, 1097 bonds, 83 residues, 1 model selected
> select add #6/A:213
1815 atoms, 1122 bonds, 84 residues, 1 model selected
> select add #6/A:214
1835 atoms, 1143 bonds, 85 residues, 1 model selected
> select add #6/A:215
1858 atoms, 1168 bonds, 86 residues, 1 model selected
> select add #6/A:332
1878 atoms, 1189 bonds, 87 residues, 1 model selected
> select add #6/A:301
1898 atoms, 1210 bonds, 88 residues, 1 model selected
> select add #6/A:300
1918 atoms, 1231 bonds, 89 residues, 1 model selected
> select add #6/A:299
1941 atoms, 1256 bonds, 90 residues, 1 model selected
> select add #6/A:298
1961 atoms, 1277 bonds, 91 residues, 1 model selected
> select add #6/A:297
1984 atoms, 1302 bonds, 92 residues, 1 model selected
> select add #6/A:296
2006 atoms, 1326 bonds, 93 residues, 1 model selected
> select add #6/A:295
2028 atoms, 1350 bonds, 94 residues, 1 model selected
> select add #6/A:294
2048 atoms, 1371 bonds, 95 residues, 1 model selected
> select add #6/A:293
2068 atoms, 1392 bonds, 96 residues, 1 model selected
> select add #6/A:292
2090 atoms, 1416 bonds, 97 residues, 1 model selected
> select add #6/A:291
2112 atoms, 1440 bonds, 98 residues, 1 model selected
> select add #6/A:290
2134 atoms, 1464 bonds, 99 residues, 1 model selected
> select add #6/A:289
2154 atoms, 1485 bonds, 100 residues, 1 model selected
> select add #6/A:288
2174 atoms, 1506 bonds, 101 residues, 1 model selected
> select add #6/A:216
2196 atoms, 1530 bonds, 102 residues, 1 model selected
> select add #6/A:217
2216 atoms, 1551 bonds, 103 residues, 1 model selected
> select add #6/A:218
2238 atoms, 1575 bonds, 104 residues, 1 model selected
> select add #6/A:219
2260 atoms, 1599 bonds, 105 residues, 1 model selected
> select add #6/A:220
2280 atoms, 1620 bonds, 106 residues, 1 model selected
> select add #6/A:287
2300 atoms, 1641 bonds, 107 residues, 1 model selected
> select add #6/A:221
2322 atoms, 1665 bonds, 108 residues, 1 model selected
> select add #6/A:286
2344 atoms, 1689 bonds, 109 residues, 1 model selected
> select add #6/A:285
2366 atoms, 1713 bonds, 110 residues, 1 model selected
> select add #6/A:284
2388 atoms, 1737 bonds, 111 residues, 1 model selected
> select add #6/A:222
2411 atoms, 1762 bonds, 112 residues, 1 model selected
> select add #6/A:223
2433 atoms, 1786 bonds, 113 residues, 1 model selected
> select add #6/A:283
2455 atoms, 1810 bonds, 114 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select ~sel & ##selected
Nothing selected
> show #6 target ab
> close #6
> show #7 models
> select #16/A:1 #7/A:1 #8/A:1 #9/A:1
92 atoms, 100 bonds, 4 residues, 4 models selected
> select #16/A:1-174 #7/A:1-174 #8/A:1-174 #9/A:1-174 #10/A #11/A:60-174
> #3/A/E:60-174
17604 atoms, 19740 bonds, 2 pseudobonds, 820 residues, 9 models selected
. [ID: 1] region 9 chains [1-174] RMSD: 231.891
> delete atoms (#7 & sel)
> delete bonds (#7 & sel)
Drag select of 22 residues, 41 shapes
> delete atoms sel
> delete bonds sel
Drag select of 7 residues, 1 pseudobonds, 18 shapes
> delete atoms (#!7 & sel)
> delete bonds (#!7 & sel)
> select #7/A:549
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #7/A:548
45 atoms, 49 bonds, 2 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #7/A:196
23 atoms, 25 bonds, 1 residue, 1 model selected
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select up
8007 atoms, 8979 bonds, 373 residues, 1 model selected
> hide sel target a
> select clear
Drag select of 33 residues
> select add #7/A:189
734 atoms, 25 bonds, 34 residues, 1 model selected
> select add #7/A:190
754 atoms, 46 bonds, 35 residues, 1 model selected
> select add #7/A:191
777 atoms, 71 bonds, 36 residues, 1 model selected
> select add #7/A:528
799 atoms, 95 bonds, 37 residues, 1 model selected
> select add #7/A:527
821 atoms, 119 bonds, 38 residues, 1 model selected
> select add #7/A:526
841 atoms, 140 bonds, 39 residues, 1 model selected
> select add #7/A:525
863 atoms, 164 bonds, 40 residues, 1 model selected
> select add #7/A:524
885 atoms, 188 bonds, 41 residues, 1 model selected
> select add #7/A:523
908 atoms, 213 bonds, 42 residues, 1 model selected
> select add #7/A:522
928 atoms, 234 bonds, 43 residues, 1 model selected
> select add #7/A:521
948 atoms, 255 bonds, 44 residues, 1 model selected
> select add #7/A:520
970 atoms, 279 bonds, 45 residues, 1 model selected
> select add #7/A:519
993 atoms, 304 bonds, 46 residues, 1 model selected
> select add #7/A:518
1013 atoms, 325 bonds, 47 residues, 1 model selected
> select add #7/A:517
1036 atoms, 350 bonds, 48 residues, 1 model selected
> select add #7/A:516
1056 atoms, 371 bonds, 49 residues, 1 model selected
> select add #7/A:192
1076 atoms, 392 bonds, 50 residues, 1 model selected
> select add #7/A:193
1098 atoms, 416 bonds, 51 residues, 1 model selected
> select add #7/A:194
1120 atoms, 440 bonds, 52 residues, 1 model selected
> select add #7/A:195
1143 atoms, 465 bonds, 53 residues, 1 model selected
> select add #7/A:196
1166 atoms, 490 bonds, 54 residues, 1 model selected
> select add #7/A:197
1186 atoms, 511 bonds, 55 residues, 1 model selected
> select add #7/A:198
1208 atoms, 535 bonds, 56 residues, 1 model selected
> select add #7/A:345
1228 atoms, 556 bonds, 57 residues, 1 model selected
> select add #7/A:344
1251 atoms, 581 bonds, 58 residues, 1 model selected
> select add #7/A:343
1274 atoms, 606 bonds, 59 residues, 1 model selected
> select add #7/A:346
1296 atoms, 630 bonds, 60 residues, 1 model selected
> select add #7/A:347
1316 atoms, 651 bonds, 61 residues, 1 model selected
> select add #7/A:342
1336 atoms, 672 bonds, 62 residues, 1 model selected
> select add #7/A:341
1356 atoms, 693 bonds, 63 residues, 1 model selected
> select add #7/A:340
1379 atoms, 718 bonds, 64 residues, 1 model selected
> select add #7/A:339
1401 atoms, 742 bonds, 65 residues, 1 model selected
> select add #7/A:338
1423 atoms, 766 bonds, 66 residues, 1 model selected
> select add #7/A:199
1443 atoms, 787 bonds, 67 residues, 1 model selected
> select add #7/A:200
1466 atoms, 812 bonds, 68 residues, 1 model selected
> select add #7/A:201
1488 atoms, 836 bonds, 69 residues, 1 model selected
> select add #7/A:202
1510 atoms, 860 bonds, 70 residues, 1 model selected
> select add #7/A:203
1532 atoms, 884 bonds, 71 residues, 1 model selected
> select add #7/A:337
1555 atoms, 909 bonds, 72 residues, 1 model selected
> select add #7/A:336
1577 atoms, 933 bonds, 73 residues, 1 model selected
> select add #7/A:335
1599 atoms, 957 bonds, 74 residues, 1 model selected
> select add #7/A:334
1621 atoms, 981 bonds, 75 residues, 1 model selected
> select add #7/A:333
1644 atoms, 1006 bonds, 76 residues, 1 model selected
> select add #7/A:332
1664 atoms, 1027 bonds, 77 residues, 1 model selected
> select add #7/A:331
1686 atoms, 1051 bonds, 78 residues, 1 model selected
> select add #7/A:204
1706 atoms, 1072 bonds, 79 residues, 1 model selected
> select add #7/A:205
1726 atoms, 1093 bonds, 80 residues, 1 model selected
> select add #7/A:206
1746 atoms, 1114 bonds, 81 residues, 1 model selected
> select add #7/A:207
1766 atoms, 1135 bonds, 82 residues, 1 model selected
> select add #7/A:208
1786 atoms, 1156 bonds, 83 residues, 1 model selected
> select add #7/A:209
1809 atoms, 1181 bonds, 84 residues, 1 model selected
> select add #7/A:210
1831 atoms, 1205 bonds, 85 residues, 1 model selected
> select add #7/A:211
1854 atoms, 1230 bonds, 86 residues, 1 model selected
> select add #7/A:303
1874 atoms, 1251 bonds, 87 residues, 1 model selected
> select add #7/A:302
1894 atoms, 1272 bonds, 88 residues, 1 model selected
> select add #7/A:301
1914 atoms, 1293 bonds, 89 residues, 1 model selected
> select add #7/A:300
1934 atoms, 1314 bonds, 90 residues, 1 model selected
> select add #7/A:299
1957 atoms, 1339 bonds, 91 residues, 1 model selected
> select add #7/A:298
1977 atoms, 1360 bonds, 92 residues, 1 model selected
> select add #7/A:297
2000 atoms, 1385 bonds, 93 residues, 1 model selected
> select add #7/A:296
2022 atoms, 1409 bonds, 94 residues, 1 model selected
> select add #7/A:295
2044 atoms, 1433 bonds, 95 residues, 1 model selected
> select add #7/A:212
2064 atoms, 1454 bonds, 96 residues, 1 model selected
> select add #7/A:213
2087 atoms, 1479 bonds, 97 residues, 1 model selected
> select add #7/A:214
2107 atoms, 1500 bonds, 98 residues, 1 model selected
> select add #7/A:215
2130 atoms, 1525 bonds, 99 residues, 1 model selected
> select add #7/A:294
2150 atoms, 1546 bonds, 100 residues, 1 model selected
> select add #7/A:217
2170 atoms, 1567 bonds, 101 residues, 1 model selected
> select add #7/A:216
2192 atoms, 1591 bonds, 102 residues, 1 model selected
> select add #7/A:293
2212 atoms, 1612 bonds, 103 residues, 1 model selected
> select add #7/A:292
2234 atoms, 1636 bonds, 104 residues, 1 model selected
> select add #7/A:291
2256 atoms, 1660 bonds, 105 residues, 1 model selected
> select add #7/A:290
2278 atoms, 1684 bonds, 106 residues, 1 model selected
> select add #7/A:289
2298 atoms, 1705 bonds, 107 residues, 1 model selected
> select add #7/A:288
2318 atoms, 1726 bonds, 108 residues, 1 model selected
> select add #7/A:287
2338 atoms, 1747 bonds, 109 residues, 1 model selected
> select add #7/A:286
2360 atoms, 1771 bonds, 110 residues, 1 model selected
> select add #7/A:285
2382 atoms, 1795 bonds, 111 residues, 1 model selected
> select add #7/A:218
2404 atoms, 1819 bonds, 112 residues, 1 model selected
> select add #7/A:219
2426 atoms, 1843 bonds, 113 residues, 1 model selected
> select add #7/A:220
2446 atoms, 1864 bonds, 114 residues, 1 model selected
> select add #7/A:221
2468 atoms, 1888 bonds, 115 residues, 1 model selected
> select add #7/A:222
2491 atoms, 1913 bonds, 116 residues, 1 model selected
> select add #7/A:223
2513 atoms, 1937 bonds, 117 residues, 1 model selected
> select add #7/A:284
2535 atoms, 1961 bonds, 118 residues, 1 model selected
> select add #7/A:283
2557 atoms, 1985 bonds, 119 residues, 1 model selected
> select add #7/A:282
2580 atoms, 2010 bonds, 120 residues, 1 model selected
> select ~sel & ##selected
5427 atoms, 6088 bonds, 253 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!2 models
Drag select of 59 residues, 2 pseudobonds
> view matrix models #7,1,0,0,327.9,0,1,0,125.68,0,0,1,110.4
> view matrix models #7,1,0,0,226.99,0,1,0,131.94,0,0,1,143.97
> view matrix models #7,1,0,0,262.06,0,1,0,151.77,0,0,1,235.68
> view matrix models #7,1,0,0,253.24,0,1,0,191.71,0,0,1,226.87
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.45894,-0.62545,0.63102,245.99,-0.83248,-0.054585,0.55136,182.73,-0.3104,-0.77835,-0.54573,232.63
> view matrix models
> #7,-0.82158,-0.56218,-0.09463,232.48,-0.56683,0.78786,0.24079,184.22,-0.060814,0.25147,-0.96595,233.66
> view matrix models
> #7,-0.68019,0.22537,0.69753,227.8,0.37654,-0.70901,0.59625,200.57,0.62893,0.66821,0.39741,234.96
> view matrix models
> #7,0.23534,-0.0087982,0.97187,239.25,0.42358,-0.89907,-0.11071,204.98,0.87476,0.43772,-0.20786,241.63
> view matrix models
> #7,0.95628,-0.25272,0.14721,253.02,-0.041787,-0.61624,-0.78645,200.86,0.28947,0.74591,-0.59986,234.64
> view matrix models
> #7,0.41136,-0.14,0.90066,242.32,0.6535,-0.64353,-0.39851,208.19,0.63539,0.75251,-0.17323,237.2
> view matrix models
> #7,0.40135,-0.15332,0.903,242.23,0.63031,-0.66908,-0.39375,207.97,0.66455,0.72721,-0.17189,237.66
> view matrix models
> #7,0.40494,-0.41099,0.81677,243.65,0.61338,-0.54035,-0.57601,208.05,0.67807,0.73424,0.033284,236.92
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.40494,-0.41099,0.81677,222.68,0.61338,-0.54035,-0.57601,213.27,0.67807,0.73424,0.033284,242.22
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.61089,-0.36018,0.70504,225.61,0.5652,-0.42518,-0.70694,212.77,0.5544,0.83035,-0.056164,240.65
> view matrix models
> #7,-0.11899,-0.62398,0.77233,216.99,0.63831,-0.64389,-0.42187,213.32,0.76053,0.44278,0.47491,242.49
> view matrix models
> #7,-0.062468,-0.66436,0.7448,217.99,0.53078,-0.65409,-0.53892,212.49,0.8452,0.36166,0.39349,244.24
> fitmap #7 inMap #2
Fit molecule fold_r_efa_model_0.cif (#7) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 2580 atoms
average map value = 2.314, steps = 304
shifted from previous position = 6.74
rotated from previous position = 18.9 degrees
atoms outside contour = 1899, contour level = 4.1986
Position of fold_r_efa_model_0.cif (#7) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
-0.99542957 0.06179645 0.07280921 195.98598978
0.00808479 -0.70514258 0.70901945 186.66807106
0.09515576 0.70636757 0.70142016 212.62408844
Axis -0.04553739 -0.38372897 -0.92232230
Axis point 93.37961520 47.65559353 0.00000000
Rotation angle (degrees) 178.33144731
Shift along axis -276.66257481
> select add #7/A:528
1286 atoms, 24 bonds, 2 pseudobonds, 60 residues, 2 models selected
> select add #7/A:191
1309 atoms, 49 bonds, 2 pseudobonds, 61 residues, 2 models selected
> select add #7/A:192
1329 atoms, 70 bonds, 2 pseudobonds, 62 residues, 2 models selected
> select add #7/A:193
1351 atoms, 94 bonds, 2 pseudobonds, 63 residues, 2 models selected
> select add #7/A:194
1373 atoms, 118 bonds, 2 pseudobonds, 64 residues, 2 models selected
> select add #7/A:195
1396 atoms, 143 bonds, 2 pseudobonds, 65 residues, 2 models selected
> select add #7/A:196
1419 atoms, 168 bonds, 2 pseudobonds, 66 residues, 2 models selected
> select add #7/A:197
1439 atoms, 189 bonds, 2 pseudobonds, 67 residues, 2 models selected
> select add #7/A:198
1461 atoms, 213 bonds, 2 pseudobonds, 68 residues, 2 models selected
> select add #7/A:343
1484 atoms, 238 bonds, 2 pseudobonds, 69 residues, 2 models selected
> select add #7/A:344
1507 atoms, 263 bonds, 2 pseudobonds, 70 residues, 2 models selected
> select add #7/A:345
1527 atoms, 284 bonds, 2 pseudobonds, 71 residues, 2 models selected
> select add #7/A:346
1549 atoms, 308 bonds, 2 pseudobonds, 72 residues, 2 models selected
> select add #7/A:347
1569 atoms, 329 bonds, 2 pseudobonds, 73 residues, 2 models selected
> select add #7/A:527
1591 atoms, 353 bonds, 2 pseudobonds, 74 residues, 2 models selected
> select add #7/A:526
1611 atoms, 374 bonds, 2 pseudobonds, 75 residues, 2 models selected
> select add #7/A:525
1633 atoms, 398 bonds, 2 pseudobonds, 76 residues, 2 models selected
> select add #7/A:524
1655 atoms, 422 bonds, 2 pseudobonds, 77 residues, 2 models selected
> select add #7/A:523
1678 atoms, 447 bonds, 2 pseudobonds, 78 residues, 2 models selected
> select add #7/A:522
1698 atoms, 468 bonds, 2 pseudobonds, 79 residues, 2 models selected
> select add #7/A:521
1718 atoms, 489 bonds, 2 pseudobonds, 80 residues, 2 models selected
> select add #7/A:520
1740 atoms, 513 bonds, 2 pseudobonds, 81 residues, 2 models selected
> select add #7/A:519
1763 atoms, 538 bonds, 2 pseudobonds, 82 residues, 2 models selected
> select add #7/A:518
1783 atoms, 559 bonds, 2 pseudobonds, 83 residues, 2 models selected
> select add #7/A:517
1806 atoms, 584 bonds, 2 pseudobonds, 84 residues, 2 models selected
> select add #7/A:516
1826 atoms, 605 bonds, 2 pseudobonds, 85 residues, 2 models selected
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R8.pdb models #7 selectedOnly
> true relModel #7
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R8.pdb
Chain information for R8.pdb #4
---
Chain | Description
A | No description available
> delete atoms (#!7 & sel)
> delete bonds (#!7 & sel)
Drag select of 85 residues, 3 pseudobonds, 255 shapes
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,178.84,0,1,0,123.78,0,0,1,298.24
> view matrix models #4,1,0,0,208.77,0,1,0,203.93,0,0,1,277.3
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.23664,-0.93138,0.27663,219.59,-0.025379,-0.29054,-0.95653,235.47,0.97127,0.21933,-0.092393,287.99
> view matrix models
> #4,0.60403,-0.71685,-0.34824,221.39,-0.44551,0.058597,-0.89336,222.88,0.66081,0.69476,-0.28397,274.93
> view matrix models
> #4,0.29571,-0.95327,0.061883,221.42,-0.66986,-0.25311,-0.69802,226.39,0.68106,0.16496,-0.7134,288.39
> view matrix models
> #4,0.44129,-0.89699,-0.025832,222.22,-0.43169,-0.18697,-0.88243,228.35,0.7867,0.40056,-0.46973,283.49
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.44129,-0.89699,-0.025832,221.98,-0.43169,-0.18697,-0.88243,203.6,0.7867,0.40056,-0.46973,263.68
> view matrix models
> #4,0.44129,-0.89699,-0.025832,227.71,-0.43169,-0.18697,-0.88243,212.72,0.7867,0.40056,-0.46973,256.85
> view matrix models
> #4,0.44129,-0.89699,-0.025832,242.11,-0.43169,-0.18697,-0.88243,217.57,0.7867,0.40056,-0.46973,250.28
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.087068,-0.87383,0.47837,235.65,-0.56111,-0.4398,-0.70124,220.91,0.82315,-0.20737,-0.52861,264.14
> view matrix models
> #4,0.083169,-0.86382,0.49689,235.32,-0.54612,-0.45659,-0.70234,221.45,0.83357,-0.21295,-0.50973,264.31
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.083169,-0.86382,0.49689,233.28,-0.54612,-0.45659,-0.70234,216.91,0.83357,-0.21295,-0.50973,267.78
> view matrix models
> #4,0.083169,-0.86382,0.49689,229.42,-0.54612,-0.45659,-0.70234,211.6,0.83357,-0.21295,-0.50973,253.29
> view matrix models
> #4,0.083169,-0.86382,0.49689,232.21,-0.54612,-0.45659,-0.70234,211.29,0.83357,-0.21295,-0.50973,253.87
> fitmap #4 inMap #2
Fit molecule R8.pdb (#4) to map cryosparc_P104_J81_mono_3dot25_map_emready.mrc
(#2) using 1826 atoms
average map value = 3.813, steps = 272
shifted from previous position = 3.67
rotated from previous position = 23.2 degrees
atoms outside contour = 1098, contour level = 4.1986
Position of R8.pdb (#4) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
-0.41193455 0.27849177 0.86761297 193.92437796
0.13314666 -0.92353531 0.35965886 205.85103928
0.90143324 0.26367568 0.34335586 223.26476200
Axis -0.54096041 -0.19061080 -0.81916382
Axis point 27.13560776 76.48832043 0.00000000
Rotation angle (degrees) 174.91028300
Shift along axis -327.03325619
> combine #4 #7
Remapping chain ID 'A' in fold_r_efa_model_0.cif #7 to 'B'
> hide #!4 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R9.pdb models #5 relModel #2
> open
> /Users/lingxiaobin/Desktop/ROOL:GOLLD/RealSpaceRefine_19/R9_real_space_refined_019.pdb
Chain information for R9_real_space_refined_019.pdb #6
---
Chain | Description
A | No description available
B | No description available
> hide #!6 models
> show #!6 models
> hide #!5 models
> select #6/A:207
20 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.56155,0.7126,0.42055,-125.55,0.16936,0.39851,-0.90139,258.07,-0.80993,0.5774,0.1031,241.2
> view matrix models
> #6,-0.33877,0.94046,-0.027863,108.25,-0.2706,-0.12575,-0.95444,456.52,-0.90111,-0.3158,0.29709,386.12
> view matrix models
> #6,-0.054339,0.99848,-0.0087084,34.877,-0.84384,-0.050582,-0.5342,476.75,-0.53383,-0.021679,0.84531,145.58
> fitmap #6 inMap #2
Fit molecule R9_real_space_refined_019.pdb (#6) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 2580 atoms
average map value = 5.888, steps = 388
shifted from previous position = 41.3
rotated from previous position = 26.7 degrees
atoms outside contour = 949, contour level = 4.1986
Position of R9_real_space_refined_019.pdb (#6) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
0.99999799 -0.00138235 -0.00144943 0.59930712
0.00138084 0.99999850 -0.00104156 -0.06574939
0.00145087 0.00103955 0.99999841 -0.53285920
Axis 0.46101471 -0.64248422 0.61211066
Axis point 364.50337386 0.00000000 415.40196387
Rotation angle (degrees) 0.12932230
Shift along axis -0.00763645
> show #!13 models
> show #!5 models
> hide #!5 models
> show #!3 models
> hide #!3 models
> show #!3 models
> open
> /Users/lingxiaobin/Desktop/ROOL:GOLLD/RealSpaceRefine_18/R7_real_space_refined_018.pdb
Chain information for R7_real_space_refined_018.pdb #12
---
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
> select #12/B:86@OP1
1 atom, 1 residue, 1 model selected
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select up
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
963 atoms, 1077 bonds, 45 residues, 1 model selected
> select up
4617 atoms, 5167 bonds, 216 residues, 1 model selected
> style sel stick
Changed 4617 atom styles
> cartoon sel
> hide #!3 models
> view matrix models
> #12,0.45399,0.53679,0.71116,-103.75,-0.35617,0.84094,-0.40738,173.75,-0.81672,-0.068346,0.57297,257.9
> view matrix models
> #12,-0.25584,0.8724,0.41649,32.268,-0.73114,0.10724,-0.67375,438,-0.63244,-0.47688,0.61041,290.54
> view matrix models
> #12,-0.38286,0.85322,0.35416,73.335,-0.59509,0.065445,-0.80099,438,-0.7066,-0.51743,0.48269,335.22
> hide #!13 models
> view matrix models
> #12,-0.16467,0.91778,0.36134,13.273,-0.72636,0.13501,-0.67393,431.71,-0.6673,-0.37344,0.6444,272.6
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.16467,0.91778,0.36134,-12.003,-0.72636,0.13501,-0.67393,454.6,-0.6673,-0.37344,0.6444,277.82
> fitmap #12 inMap #2
Fit molecule R7_real_space_refined_018.pdb (#12) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 4617 atoms
average map value = 1.04, steps = 400
shifted from previous position = 38.6
rotated from previous position = 29.6 degrees
atoms outside contour = 4170, contour level = 4.1986
Position of R7_real_space_refined_018.pdb (#12) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
0.95328633 -0.25085292 0.16827947 58.35692875
0.15933647 0.89087250 0.42539166 -73.75589940
-0.25662629 -0.37870700 0.88922660 157.19416869
Axis -0.80596466 0.42589179 0.41114128
Axis point 0.00000000 356.64991123 251.04350874
Rotation angle (degrees) 29.92344238
Shift along axis -13.81664315
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.17783,0.93424,0.30916,-48.816,-0.80909,0.31763,-0.49446,414.51,-0.56014,-0.1622,0.81236,204.6
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.17783,0.93424,0.30916,-43.287,-0.80909,0.31763,-0.49446,434.15,-0.56014,-0.1622,0.81236,230.79
> ui mousemode right "rotate selected models"
> fitmap #12 inMap #2
Fit molecule R7_real_space_refined_018.pdb (#12) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 4617 atoms
average map value = 5.857, steps = 216
shifted from previous position = 8.58
rotated from previous position = 36.2 degrees
atoms outside contour = 1682, contour level = 4.1986
Position of R7_real_space_refined_018.pdb (#12) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
0.99999926 -0.00075134 -0.00096113 0.31810592
0.00075094 0.99999963 -0.00041652 -0.09178572
0.00096144 0.00041580 0.99999945 -0.29195584
Axis 0.32286003 -0.74577211 0.58273953
Axis point 304.47251710 0.00000000 330.39320366
Rotation angle (degrees) 0.07385297
Shift along axis 0.00102071
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> combine #6 #12
Remapping chain ID 'A' in R7_real_space_refined_018.pdb #12 to 'G'
Remapping chain ID 'B' in R7_real_space_refined_018.pdb #12 to 'H'
> hide #!6 models
> hide #!12 models
> close #6
> close #12
> close #13
> show #16 models
> hide #16 models
> show #10 models
> hide #10 models
> close #10
> show #!11 models
> hide #!11 models
> show #!11 models
> close #11
> show #!5 models
> hide #!5 models
> close #5
> show #!4 models
> hide #!14 models
> show #!14 models
> close #4
> show #!3 models
> hide #!3 models
> close #3
> show #16 models
> hide #16 models
> show #!7 models
> hide #!7 models
> close #7
> show #8 models
Drag select of 88 residues, 169 shapes
> ui mousemode right "translate selected models"
> view matrix models #8,1,0,0,248.7,0,1,0,330.53,0,0,1,114.32
> view matrix models #8,1,0,0,276.63,0,1,0,201.86,0,0,1,227.02
> view matrix models #8,1,0,0,323.24,0,1,0,165.12,0,0,1,245.82
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.32423,0.92269,0.20862,333.42,0.78558,0.38548,-0.48402,158.87,-0.52702,0.0069542,-0.84983,248.48
> view matrix models
> #8,-0.81458,-0.084499,0.57386,337.03,-0.037478,0.99493,0.093301,165.44,-0.57883,0.054494,-0.81362,248.9
> view matrix models
> #8,0.094461,-0.34148,0.93513,330.51,0.99156,-0.05157,-0.11899,157.43,0.088858,0.93847,0.33372,244.98
> view matrix models
> #8,0.55534,-0.58844,0.58766,326.84,0.55218,-0.26749,-0.78965,160.16,0.62185,0.76301,0.17637,240.93
> select up
12448 atoms, 13961 bonds, 580 residues, 1 model selected
> hide sel target a
> select clear
> select #8/A:281
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #8/A:280
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add #8/A:279
62 atoms, 66 bonds, 3 residues, 1 model selected
> select add #8/A:224
82 atoms, 87 bonds, 4 residues, 1 model selected
> select add #8/A:225
105 atoms, 112 bonds, 5 residues, 1 model selected
> select add #8/A:226
125 atoms, 133 bonds, 6 residues, 1 model selected
> select add #8/A:227
145 atoms, 154 bonds, 7 residues, 1 model selected
> select add #8/A:228
165 atoms, 175 bonds, 8 residues, 1 model selected
> select add #8/A:229
185 atoms, 196 bonds, 9 residues, 1 model selected
> select add #8/A:230
207 atoms, 220 bonds, 10 residues, 1 model selected
> select add #8/A:231
230 atoms, 245 bonds, 11 residues, 1 model selected
> select add #8/A:232
250 atoms, 266 bonds, 12 residues, 1 model selected
> select add #8/A:233
273 atoms, 291 bonds, 13 residues, 1 model selected
> select add #8/A:234
296 atoms, 316 bonds, 14 residues, 1 model selected
> select add #8/A:235
318 atoms, 340 bonds, 15 residues, 1 model selected
> select add #8/A:236
341 atoms, 365 bonds, 16 residues, 1 model selected
> select add #8/A:237
363 atoms, 389 bonds, 17 residues, 1 model selected
> select add #8/A:238
385 atoms, 413 bonds, 18 residues, 1 model selected
> select add #8/A:239
405 atoms, 434 bonds, 19 residues, 1 model selected
> select add #8/A:240
427 atoms, 458 bonds, 20 residues, 1 model selected
> select add #8/A:241
449 atoms, 482 bonds, 21 residues, 1 model selected
> select add #8/A:242
469 atoms, 503 bonds, 22 residues, 1 model selected
> select add #8/A:243
489 atoms, 524 bonds, 23 residues, 1 model selected
> select add #8/A:244
509 atoms, 545 bonds, 24 residues, 1 model selected
> show #!1 models
> hide #!1 models
> select add #8/A:245
531 atoms, 569 bonds, 25 residues, 1 model selected
> select add #8/A:246
553 atoms, 593 bonds, 26 residues, 1 model selected
> select add #8/A:247
576 atoms, 618 bonds, 27 residues, 1 model selected
> select add #8/A:248
596 atoms, 639 bonds, 28 residues, 1 model selected
> select add #8/A:249
616 atoms, 660 bonds, 29 residues, 1 model selected
> select add #8/A:250
638 atoms, 684 bonds, 30 residues, 1 model selected
> select add #8/A:251
661 atoms, 709 bonds, 31 residues, 1 model selected
> select add #8/A:252
684 atoms, 734 bonds, 32 residues, 1 model selected
> select add #8/A:253
704 atoms, 755 bonds, 33 residues, 1 model selected
> select add #8/A:278
724 atoms, 776 bonds, 34 residues, 1 model selected
> select add #8/A:277
744 atoms, 797 bonds, 35 residues, 1 model selected
> select add #8/A:276
766 atoms, 821 bonds, 36 residues, 1 model selected
> select add #8/A:275
789 atoms, 846 bonds, 37 residues, 1 model selected
> select add #8/A:274
811 atoms, 870 bonds, 38 residues, 1 model selected
> select add #8/A:273
831 atoms, 891 bonds, 39 residues, 1 model selected
> select add #8/A:272
854 atoms, 916 bonds, 40 residues, 1 model selected
> select add #8/A:271
877 atoms, 941 bonds, 41 residues, 1 model selected
> select add #8/A:270
897 atoms, 962 bonds, 42 residues, 1 model selected
> select add #8/A:269
917 atoms, 983 bonds, 43 residues, 1 model selected
> select add #8/A:254
940 atoms, 1008 bonds, 44 residues, 1 model selected
> select add #8/A:255
963 atoms, 1033 bonds, 45 residues, 1 model selected
> select add #8/A:256
985 atoms, 1057 bonds, 46 residues, 1 model selected
> select add #8/A:257
1007 atoms, 1081 bonds, 47 residues, 1 model selected
> select add #8/A:258
1030 atoms, 1106 bonds, 48 residues, 1 model selected
> select add #8/A:259
1050 atoms, 1127 bonds, 49 residues, 1 model selected
> select add #8/A:260
1073 atoms, 1152 bonds, 50 residues, 1 model selected
> select add #8/A:261
1093 atoms, 1173 bonds, 51 residues, 1 model selected
> select add #8/A:262
1116 atoms, 1198 bonds, 52 residues, 1 model selected
> select add #8/A:263
1138 atoms, 1222 bonds, 53 residues, 1 model selected
> select add #8/A:264
1161 atoms, 1247 bonds, 54 residues, 1 model selected
> select add #8/A:265
1183 atoms, 1271 bonds, 55 residues, 1 model selected
> select add #8/A:266
1205 atoms, 1295 bonds, 56 residues, 1 model selected
> select add #8/A:267
1228 atoms, 1320 bonds, 57 residues, 1 model selected
> select add #8/A:268
1248 atoms, 1341 bonds, 58 residues, 1 model selected
> select ~sel & ##selected
11200 atoms, 12563 bonds, 522 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!1 models
> select add #14/A:286
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #14/A:285
44 atoms, 48 bonds, 2 residues, 1 model selected
> select add #14/A:284
66 atoms, 72 bonds, 3 residues, 1 model selected
> select add #14/A:283
88 atoms, 96 bonds, 4 residues, 1 model selected
> select add #14/A:282
111 atoms, 121 bonds, 5 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #14,-0.24289,0.96982,0.02118,80.359,-0.53737,-0.11634,-0.83528,520.4,-0.80761,-0.21426,0.54941,330.21
> ui mousemode right "translate selected atoms"
> fitmap #14 inMap #1
Fit molecule combination (#14) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 7197 atoms
average map value = 3.773, steps = 152
shifted from previous position = 7.71
rotated from previous position = 18.1 degrees
atoms outside contour = 3521, contour level = 4.3314
Position of combination (#14) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.49091870 0.86159345 0.12905638 134.27648360
-0.59615186 -0.22419886 -0.77093309 539.08566867
-0.63529661 -0.45540267 0.62370396 322.83968918
Axis 0.18826932 0.45607083 -0.86980116
Axis point 271.45260187 311.76846103 0.00000000
Rotation angle (degrees) 123.07297734
Shift along axis -9.66494613
> select subtract #14/A:286
89 atoms, 97 bonds, 4 residues, 1 model selected
> select subtract #14/A:285
67 atoms, 73 bonds, 3 residues, 1 model selected
> select subtract #14/A:283
45 atoms, 49 bonds, 2 residues, 1 model selected
> select subtract #14/A:284
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #14/A:284
45 atoms, 49 bonds, 2 residues, 1 model selected
> select add #14/A:283
67 atoms, 73 bonds, 3 residues, 1 model selected
> select clear
> select add #14/A:283
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #14/A:282
45 atoms, 49 bonds, 2 residues, 1 model selected
> select add #14/A:286
67 atoms, 73 bonds, 3 residues, 1 model selected
> select clear
> select #8/A:226
20 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.55534,-0.58844,0.58766,255.08,0.55218,-0.26749,-0.78965,253.42,0.62185,0.76301,0.17637,238.83
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.56491,-0.58098,0.58595,254.66,0.56439,-0.24597,-0.78801,252.22,0.60195,0.77586,0.18895,238.16
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.56491,-0.58098,0.58595,260.96,0.56439,-0.24597,-0.78801,244.82,0.60195,0.77586,0.18895,250.23
> hide #!1 models
> select add #8/A:224
40 atoms, 42 bonds, 2 residues, 1 model selected
> select add #8/A:225
63 atoms, 67 bonds, 3 residues, 1 model selected
> select add #8/A:227
83 atoms, 88 bonds, 4 residues, 1 model selected
> select add #8/A:228
103 atoms, 109 bonds, 5 residues, 1 model selected
> select add #8/A:229
123 atoms, 130 bonds, 6 residues, 1 model selected
> select add #8/A:230
145 atoms, 154 bonds, 7 residues, 1 model selected
> select add #8/A:231
168 atoms, 179 bonds, 8 residues, 1 model selected
> select add #8/A:232
188 atoms, 200 bonds, 9 residues, 1 model selected
> select add #8/A:233
211 atoms, 225 bonds, 10 residues, 1 model selected
> select add #8/A:234
234 atoms, 250 bonds, 11 residues, 1 model selected
> select add #8/A:235
256 atoms, 274 bonds, 12 residues, 1 model selected
> select add #8/A:236
279 atoms, 299 bonds, 13 residues, 1 model selected
> select add #8/A:237
301 atoms, 323 bonds, 14 residues, 1 model selected
> select add #8/A:238
323 atoms, 347 bonds, 15 residues, 1 model selected
> select add #8/A:239
343 atoms, 368 bonds, 16 residues, 1 model selected
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R10.pdb models #8
> selectedOnly true relModel #8
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R10.pdb
Chain information for R10.pdb #3
---
Chain | Description
A | No description available
> delete atoms sel
> delete bonds sel
Drag select of 16 residues, 48 shapes
> view matrix models #3,1,0,0,43.787,0,1,0,60.274,0,0,1,371.8
> show #!1 models
> show #!2 models
> view matrix models #3,1,0,0,34.915,0,1,0,70.493,0,0,1,348.53
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,79.924,0,1,0,71.155,0,0,1,374.99
> view matrix models #3,1,0,0,133.59,0,1,0,72.403,0,0,1,406.94
> view matrix models #3,1,0,0,222.44,0,1,0,41.156,0,0,1,360.28
> view matrix models #3,1,0,0,155.12,0,1,0,74.668,0,0,1,296.63
> view matrix models #3,1,0,0,216.83,0,1,0,92.336,0,0,1,297.89
> view matrix models #3,1,0,0,199.99,0,1,0,141.46,0,0,1,298.8
> view matrix models #3,1,0,0,209.74,0,1,0,141.15,0,0,1,299.06
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.76301,-0.56591,-0.31234,243.89,0.38276,0.78495,-0.48718,152.19,0.52087,0.25217,0.81554,282.02
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.76301,-0.56591,-0.31234,246.29,0.38276,0.78495,-0.48718,158.05,0.52087,0.25217,0.81554,300.79
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 3 atomic models, 2 maps.
> hide #!2 models
> fitmap #3 inMap #1
Fit molecule R10.pdb (#3) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 343 atoms
average map value = 4.902, steps = 212
shifted from previous position = 8.52
rotated from previous position = 104 degrees
atoms outside contour = 97, contour level = 4.3314
Position of R10.pdb (#3) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.37225400 -0.58644929 0.71937765 247.39634593
0.92448863 -0.16569062 0.34331820 253.75795722
-0.08214458 0.79285803 0.60384469 255.03587156
Axis 0.25419820 0.45323128 0.85437971
Axis point 59.52593126 111.00867808 0.00000000
Rotation angle (degrees) 117.84297305
Shift along axis 395.79622310
> select #8/A:267
23 atoms, 25 bonds, 1 residue, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.27205,-0.5024,0.82072,255,0.55794,-0.77724,-0.29084,293.93,0.78402,0.37879,0.49176,286.64
> view matrix models
> #8,-0.66065,-0.58339,0.47244,242.51,0.41314,-0.80801,-0.42003,289.33,0.62678,-0.082313,0.77484,322.08
> view matrix models
> #8,-0.1342,-0.99026,-0.037078,254.07,0.68188,-0.065126,-0.72856,237.77,0.71905,-0.12305,0.68398,322.26
> view matrix models
> #8,0.26585,-0.90191,0.34041,267.32,0.89835,0.1037,-0.42686,241.38,0.34969,0.41929,0.8378,291.7
> view matrix models
> #8,-0.1169,-0.98545,0.12338,259.82,0.86683,-0.16187,-0.47159,254.95,0.4847,0.051826,0.87314,316.11
> fitmap #8 inMap #1
Fit molecule fold_r_efa_model_0.cif (#8) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 905 atoms
average map value = 3.162, steps = 188
shifted from previous position = 12
rotated from previous position = 12.5 degrees
atoms outside contour = 567, contour level = 4.3314
Position of fold_r_efa_model_0.cif (#8) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.17957719 -0.98371791 -0.00714856 242.79993995
0.93151157 -0.16770162 -0.32274194 257.98932332
0.31628820 -0.06461605 0.94646001 322.19149109
Axis 0.13173556 -0.16506722 0.97744491
Axis point -28.99214806 240.82929557 0.00000000
Rotation angle (degrees) 101.56090087
Shift along axis 304.32423828
> view matrix models
> #8,0.37851,-0.83186,-0.40588,226.01,0.76596,0.5277,-0.36721,213.67,0.51965,-0.1719,0.83691,326.9
> view matrix models
> #8,-0.053845,-0.98068,-0.18804,237.54,0.95472,0.0046173,-0.29746,249.08,0.29258,-0.19555,0.93603,329.21
> view matrix models
> #8,-0.53425,-0.51002,0.67413,235.59,0.78905,-0.58699,0.18123,299.18,0.30328,0.62875,0.71603,273.04
> view matrix models
> #8,-0.28661,-0.83292,0.4734,250.15,0.91373,-0.3862,-0.12629,277.72,0.28802,0.39636,0.87175,292.13
> view matrix models
> #8,0.32397,-0.9442,0.059448,248.85,0.90576,0.2914,-0.30771,231.33,0.27321,0.15353,0.94962,309.02
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.32397,-0.9442,0.059448,244.23,0.90576,0.2914,-0.30771,236.85,0.27321,0.15353,0.94962,303.21
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.044163,-0.91703,0.39636,250.53,0.90124,-0.20777,-0.38027,263.41,0.43107,0.34042,0.83564,289.98
> view matrix models
> #8,-0.093448,-0.87872,0.4681,250.31,0.89802,-0.27741,-0.34148,268.86,0.42992,0.38845,0.81503,286.41
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.093448,-0.87872,0.4681,253.22,0.89802,-0.27741,-0.34148,266.06,0.42992,0.38845,0.81503,291.35
> view matrix models
> #8,-0.093448,-0.87872,0.4681,252.7,0.89802,-0.27741,-0.34148,262.88,0.42992,0.38845,0.81503,289.67
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.47705,-0.56778,0.67085,237.31,0.70947,-0.6993,-0.087351,294.6,0.51872,0.43428,0.73643,285.18
> view matrix models
> #8,-0.75248,-0.17444,0.63509,209.72,0.44035,-0.85031,0.28819,313.91,0.48976,0.49652,0.71666,280.47
> view matrix models
> #8,-0.77861,-0.25508,0.57332,211.89,0.47942,-0.83131,0.28122,313,0.40487,0.49382,0.76956,281.55
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.77861,-0.25508,0.57332,214,0.47942,-0.83131,0.28122,321.38,0.40487,0.49382,0.76956,280.52
> view matrix models
> #8,-0.77861,-0.25508,0.57332,216.12,0.47942,-0.83131,0.28122,320.86,0.40487,0.49382,0.76956,282.3
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.7988,-0.12481,0.5885,208.8,0.40369,-0.8365,0.37054,323.52,0.44604,0.53356,0.71858,278.6
> view matrix models
> #8,-0.88438,0.2226,0.41028,180.96,-0.05392,-0.9218,0.38391,323.6,0.46365,0.3174,0.82722,295.42
> view matrix models
> #8,-0.90003,-0.032803,0.43458,196.63,0.20756,-0.90908,0.36124,325.12,0.38322,0.41533,0.82501,288.65
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.90003,-0.032803,0.43458,199.49,0.20756,-0.90908,0.36124,325.71,0.38322,0.41533,0.82501,293.95
> view matrix models
> #8,-0.90003,-0.032803,0.43458,199.09,0.20756,-0.90908,0.36124,327.58,0.38322,0.41533,0.82501,293.18
> view matrix models
> #8,-0.90003,-0.032803,0.43458,199.77,0.20756,-0.90908,0.36124,327.18,0.38322,0.41533,0.82501,290.88
> fitmap #8 inMap #1
Fit molecule fold_r_efa_model_0.cif (#8) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 905 atoms
average map value = 2.58, steps = 76
shifted from previous position = 3.98
rotated from previous position = 6.91 degrees
atoms outside contour = 624, contour level = 4.3314
Position of fold_r_efa_model_0.cif (#8) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.89625850 -0.04060624 0.44166936 201.90769458
0.26173313 -0.85235276 0.45275881 328.12015979
0.35807327 0.52138844 0.77455641 286.17576522
Axis 0.21373058 0.26034008 0.94156374
Axis point 58.84099395 129.50977676 0.00000000
Rotation angle (degrees) 170.76107824
Shift along axis 398.02940100
> volume #1 level 3.217
> select #3/A:226
20 atoms, 21 bonds, 1 residue, 1 model selected
> view matrix models
> #3,-0.37225,-0.58645,0.71938,225.83,0.92449,-0.16569,0.34332,270.96,-0.082145,0.79286,0.60384,226.2
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.80866,-0.33238,0.48538,214.43,0.3396,0.93748,0.076184,177.24,-0.48035,0.10323,0.87098,278.81
> view matrix models
> #3,-0.46275,-0.88428,-0.062517,232.51,0.081092,-0.11245,0.99034,270.31,-0.88277,0.45321,0.12374,234.52
> view matrix models
> #3,-0.51478,-0.15016,-0.84407,162.33,0.39352,-0.91609,-0.077021,313.94,-0.76168,-0.3718,0.53067,305.28
> view matrix models
> #3,-0.28204,-1.415e-05,-0.9594,151.32,0.61696,-0.76581,-0.18136,303.03,-0.73472,-0.64306,0.216,320.06
> view matrix models
> #3,0.44713,-0.11971,-0.88642,169.07,0.73633,-0.51339,0.44075,296.81,-0.50784,-0.84977,-0.14141,331.27
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.44713,-0.11971,-0.88642,171.28,0.73633,-0.51339,0.44075,298.46,-0.50784,-0.84977,-0.14141,311.69
> view matrix models
> #3,0.44713,-0.11971,-0.88642,182.16,0.73633,-0.51339,0.44075,308.24,-0.50784,-0.84977,-0.14141,323.61
> view matrix models
> #3,0.44713,-0.11971,-0.88642,186.52,0.73633,-0.51339,0.44075,307.39,-0.50784,-0.84977,-0.14141,312.59
> view matrix models
> #3,0.44713,-0.11971,-0.88642,186.25,0.73633,-0.51339,0.44075,307.82,-0.50784,-0.84977,-0.14141,310.19
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.28945,0.58265,-0.75943,134.32,0.92429,0.036082,0.37997,267.39,0.24879,-0.81192,-0.5281,308.02
> view matrix models
> #3,0.12422,0.64341,-0.75538,128.14,0.94894,0.14544,0.27994,257.6,0.28998,-0.75158,-0.59249,302.73
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.12422,0.64341,-0.75538,131.39,0.94894,0.14544,0.27994,256.78,0.28998,-0.75158,-0.59249,304.86
> fitmap #3 inMap #1
Fit molecule R10.pdb (#3) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 343 atoms
average map value = 4.662, steps = 164
shifted from previous position = 4.08
rotated from previous position = 39.6 degrees
atoms outside contour = 57, contour level = 3.2169
Position of R10.pdb (#3) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.27331747 0.80793578 -0.52205108 124.92829142
0.93004064 -0.36052494 -0.07103643 287.21089444
-0.24560530 -0.46611323 -0.84995087 276.69167362
Axis -0.79426657 -0.55576951 0.24548090
Axis point -0.00000000 125.63069342 143.24837288
Rotation angle (degrees) 165.59908113
Shift along axis -190.92690244
> view matrix models
> #3,0.27332,0.80794,-0.52205,124.91,0.93004,-0.36052,-0.071036,287.24,-0.24561,-0.46611,-0.84995,276.78
> view matrix models
> #3,0.27332,0.80794,-0.52205,145.41,0.93004,-0.36052,-0.071036,273.4,-0.24561,-0.46611,-0.84995,312.03
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.64291,0.18872,-0.74233,178.44,-0.32205,-0.94594,0.038441,306.54,-0.69494,0.26378,0.66893,280.75
> view matrix models
> #3,-0.3731,-0.72826,0.57483,274.3,0.9229,-0.35485,0.14945,276.87,0.095137,0.58627,0.80451,267.14
> view matrix models
> #3,-0.33674,-0.90907,0.24535,282.09,0.90101,-0.38677,-0.19645,272.6,0.27348,0.15491,0.94932,303.93
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.33674,-0.90907,0.24535,279.47,0.90101,-0.38677,-0.19645,276.77,0.27348,0.15491,0.94932,313.86
> fitmap #3 inMap #1
Fit molecule R10.pdb (#3) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 343 atoms
average map value = 4.247, steps = 280
shifted from previous position = 19
rotated from previous position = 96.9 degrees
atoms outside contour = 91, contour level = 3.2169
Position of R10.pdb (#3) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.32918070 -0.30515323 -0.89360034 206.72351645
0.63820019 0.76937433 -0.02763414 179.40477890
0.69594581 -0.56119928 0.44801203 368.17607122
Axis -0.27733993 -0.82622453 0.49034231
Axis point -231.50195556 -0.00000000 397.35655380
Rotation angle (degrees) 74.14024971
Shift along axis -25.02900783
> view matrix models
> #3,0.32918,-0.30515,-0.8936,206.99,0.6382,0.76937,-0.027634,174.82,0.69595,-0.5612,0.44801,359.89
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.4007,-0.77345,0.49114,260.58,0.91425,-0.37259,0.15913,267.03,0.059917,0.51279,0.85642,280.22
> view matrix models
> #3,-0.83338,-0.059368,0.54951,203.71,0.3404,-0.83842,0.42566,300.97,0.43545,0.54179,0.71893,279.33
> view matrix models
> #3,-0.7403,-0.59725,0.30862,240.54,0.64458,-0.761,0.073472,291.77,0.19098,0.25332,0.94834,302.69
> view matrix models
> #3,-0.75638,-0.60234,-0.25511,230.37,0.26797,-0.64109,0.71916,290.82,-0.59673,0.4756,0.64631,272.38
> view matrix models
> #3,-0.93991,0.30543,-0.15261,162.11,-0.30101,-0.53031,0.79257,278.03,0.16114,0.79087,0.59038,255.39
> view matrix models
> #3,-0.92081,0.05007,0.38679,191.5,0.33345,-0.41335,0.84732,276.73,0.2023,0.9092,0.36392,242.72
> view matrix models
> #3,-0.82662,-0.45762,0.32754,229.48,0.55326,-0.55433,0.62179,285.38,-0.10298,0.6952,0.71141,262.11
> fitmap #3 inMap #1
Fit molecule R10.pdb (#3) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 343 atoms
average map value = 4.916, steps = 160
shifted from previous position = 5.77
rotated from previous position = 29.7 degrees
atoms outside contour = 45, contour level = 3.2169
Position of R10.pdb (#3) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.75516252 -0.25383303 0.60439916 215.71265248
0.65051879 -0.17630014 0.73874459 260.13151985
-0.08096212 0.95104524 0.29825842 239.93545107
Axis 0.18390531 0.59369380 0.78339422
Axis point 72.94090039 68.64442247 0.00000000
Rotation angle (degrees) 144.74608589
Shift along axis 382.07321979
> select #8/A:253
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #8/A:253
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #8/A:253
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #8/A:253
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #8/A:253
20 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
> select #8/A:252
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #8/A:278
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add #8/A:251
66 atoms, 71 bonds, 3 residues, 1 model selected
> select add #8/A:250
88 atoms, 95 bonds, 4 residues, 1 model selected
> select add #8/A:249
108 atoms, 116 bonds, 5 residues, 1 model selected
> select add #8/A:248
128 atoms, 137 bonds, 6 residues, 1 model selected
> select add #8/A:247
151 atoms, 162 bonds, 7 residues, 1 model selected
> select add #8/A:246
173 atoms, 186 bonds, 8 residues, 1 model selected
> select add #8/A:245
195 atoms, 210 bonds, 9 residues, 1 model selected
> select add #8/A:244
215 atoms, 231 bonds, 10 residues, 1 model selected
> select add #8/A:243
235 atoms, 252 bonds, 11 residues, 1 model selected
> select add #8/A:242
255 atoms, 273 bonds, 12 residues, 1 model selected
> select add #8/A:241
277 atoms, 297 bonds, 13 residues, 1 model selected
> select add #8/A:240
299 atoms, 321 bonds, 14 residues, 1 model selected
> select add #8/A:279
319 atoms, 342 bonds, 15 residues, 1 model selected
> select add #8/A:280
339 atoms, 363 bonds, 16 residues, 1 model selected
> select add #8/A:281
361 atoms, 387 bonds, 17 residues, 1 model selected
> select add #8/A:277
381 atoms, 408 bonds, 18 residues, 1 model selected
> select subtract #8/A:277
361 atoms, 387 bonds, 17 residues, 1 model selected
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R11.pdb models #8
> selectedOnly true relModel #8
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R11.pdb
Chain information for R11.pdb #4
---
Chain | Description
A | No description available
> delete atoms sel
> delete bonds sel
Drag select of 17 residues, 1 pseudobonds, 51 shapes
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,171.06,0,1,0,123.02,0,0,1,369.18
> view matrix models #4,1,0,0,140.23,0,1,0,147.23,0,0,1,324.36
> view matrix models #4,1,0,0,135.71,0,1,0,167.47,0,0,1,302.02
> view matrix models #4,1,0,0,178,0,1,0,184.62,0,0,1,283.41
> view matrix models #4,1,0,0,205.55,0,1,0,170.55,0,0,1,308.94
> view matrix models #4,1,0,0,206,0,1,0,195.15,0,0,1,302.59
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.67665,-0.015784,-0.73614,169.95,-0.018819,0.99907,-0.038721,193.18,0.73607,0.040054,0.67572,301.91
> view matrix models
> #4,0.98891,-0.13528,-0.061276,211.03,0.11084,0.94694,-0.30169,187.78,0.098837,0.29156,0.95143,286.2
> view matrix models
> #4,0.05463,0.99835,-0.017433,128.97,-0.67206,0.023852,-0.74011,205.02,-0.73848,0.052148,0.67226,270.53
> view matrix models
> #4,0.94515,0.22651,-0.23532,181.6,-0.30558,0.3588,-0.88198,187.87,-0.11534,0.90551,0.40834,224.01
> view matrix models
> #4,0.98234,-0.12176,-0.14209,205.77,-0.082682,0.39875,-0.91333,188.86,0.16787,0.90894,0.38164,228.42
> view matrix models
> #4,0.68516,-0.061895,-0.72576,171.98,-0.66905,0.34045,-0.66066,190.77,0.28798,0.93822,0.19185,221.27
> view matrix models
> #4,0.6816,0.71067,0.17426,166.19,-0.41329,0.57043,-0.70979,181.18,-0.60383,0.41177,0.68252,252.71
> view matrix models
> #4,0.95869,0.25119,0.1335,196.27,-0.12187,0.78675,-0.60512,179.47,-0.25703,0.56385,0.78486,255.75
> fitmap #4 inMap #1
Fit molecule R11.pdb (#4) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 361 atoms
average map value = 3.792, steps = 184
shifted from previous position = 10.2
rotated from previous position = 31.9 degrees
atoms outside contour = 121, contour level = 3.2169
Position of R11.pdb (#4) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.77573429 0.62677279 -0.07343147 170.58711351
-0.60693468 0.70914376 -0.35881111 185.40717181
-0.17281957 0.32291018 0.93051728 271.62433929
Axis 0.48245324 0.07033683 -0.87309312
Axis point 430.78798824 -227.18573397 0.00000000
Rotation angle (degrees) 44.95210155
Shift along axis -141.81208449
> view matrix models
> #4,0.74895,0.65336,-0.11043,166.98,-0.64414,0.67878,-0.35261,186.58,-0.15543,0.33522,0.92923,271.25
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.74895,0.65336,-0.11043,168.04,-0.64414,0.67878,-0.35261,185.18,-0.15543,0.33522,0.92923,279.15
> fitmap #4 inMap #1
Fit molecule R11.pdb (#4) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 361 atoms
average map value = 3.793, steps = 128
shifted from previous position = 8.09
rotated from previous position = 3.03 degrees
atoms outside contour = 122, contour level = 3.2169
Position of R11.pdb (#4) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.77543005 0.62720355 -0.07296531 170.58617857
-0.60734832 0.70924530 -0.35790937 185.43122922
-0.17273173 0.32184904 0.93090115 271.71720168
Axis 0.48112591 0.07061363 -0.87380294
Axis point 430.50650250 -226.96343630 0.00000000
Rotation angle (degrees) 44.94475478
Shift along axis -142.25988629
> view matrix models
> #4,0.77543,0.6272,-0.072965,170.29,-0.60735,0.70925,-0.35791,182.35,-0.17273,0.32185,0.9309,279.94
> select clear
> select #4/A:246
22 atoms, 24 bonds, 1 residue, 1 model selected
> view matrix models
> #4,0.77543,0.6272,-0.072965,170.29,-0.60735,0.70925,-0.35791,182.34,-0.17273,0.32185,0.9309,279.91
> view matrix models
> #4,0.77543,0.6272,-0.072965,169.61,-0.60735,0.70925,-0.35791,180.2,-0.17273,0.32185,0.9309,281.49
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.95726,-0.099899,-0.27143,166.08,-0.25079,-0.18082,0.951,291.7,-0.14408,0.97843,0.14804,212.74
> view matrix models
> #4,-0.52018,0.63245,0.57395,169.41,0.26361,-0.52032,0.81227,315.36,0.81236,0.57382,0.10394,253.1
> view matrix models
> #4,0.0032449,0.42027,0.90739,206.39,0.10918,-0.90212,0.41744,317.08,0.99402,0.097711,-0.04881,277.32
> view matrix models
> #4,-0.67038,0.20673,0.71264,196.3,0.28782,-0.81277,0.50652,319.46,0.68392,0.54467,0.48537,267.82
> view matrix models
> #4,-0.55381,0.63645,0.53687,167.04,0.05742,-0.61405,0.78718,315.27,0.83066,0.46677,0.30352,267.62
> view matrix models
> #4,0.305,0.4152,0.85708,210.69,0.014622,-0.9019,0.4317,315.79,0.95224,-0.11914,-0.28115,278.83
> view matrix models
> #4,0.30824,0.53661,0.78552,200.83,0.093742,-0.83883,0.53625,318.22,0.94668,-0.091658,-0.30886,275.97
> view matrix models
> #4,0.11326,0.5617,0.81955,196.88,0.10382,-0.82703,0.55249,318.44,0.98813,0.022514,-0.15199,276.96
> view matrix models
> #4,0.90475,0.024385,0.42524,227.32,0.10932,-0.97821,-0.17649,296.96,0.41167,0.20617,-0.88771,224.56
> view matrix models
> #4,0.035253,0.49648,0.86733,200.57,0.59877,-0.70535,0.37942,314.62,0.80015,0.50595,-0.32214,238.73
> view matrix models
> #4,-0.2972,-0.086377,0.9509,230.08,0.48874,-0.8693,0.073787,308.84,0.82025,0.48667,0.30057,266.07
> view matrix models
> #4,-0.049287,-0.78331,0.61968,261.03,0.37433,-0.5897,-0.71564,257.96,0.92599,0.19669,0.32228,285.62
> view matrix models
> #4,0.39196,-0.36505,0.84446,256.05,0.52004,-0.66927,-0.53069,273.22,0.7589,0.64716,-0.072486,240.15
> view matrix models
> #4,0.76347,-0.29567,0.57419,248.72,0.22093,-0.71586,-0.66237,264.3,0.60688,0.63256,-0.48121,220.95
> view matrix models
> #4,0.62583,0.71209,0.31821,178.38,0.76582,-0.48367,-0.42378,272.29,-0.14786,0.50891,-0.84803,197.13
> view matrix models
> #4,0.74559,-0.15772,0.64747,243.63,0.33233,-0.75415,-0.5664,272.65,0.57762,0.63748,-0.50987,218.91
> view matrix models
> #4,0.69867,0.48018,0.53036,201.5,0.62901,-0.059065,-0.77515,230.59,-0.34089,0.87518,-0.3433,193.51
> view matrix models
> #4,0.8445,-0.50507,0.1781,245.79,0.17631,-0.051833,-0.98297,212.09,0.5057,0.86152,0.045275,227.84
> view matrix models
> #4,0.5648,-0.75961,0.32248,260.04,0.20168,-0.25187,-0.94651,225.54,0.8002,0.59963,0.01094,247.36
> view matrix models
> #4,0.55207,-0.53898,0.63618,260.35,0.49237,-0.40502,-0.77041,247.69,0.6729,0.73855,0.041779,238.09
> view matrix models
> #4,0.31834,-0.73939,0.59326,264.86,0.52105,-0.38633,-0.76109,247.61,0.79194,0.55141,0.26227,260.34
> view matrix models
> #4,0.066064,-0.86969,0.48915,262.62,0.5239,-0.38698,-0.7588,247.8,0.84921,0.30639,0.43007,282.49
> view matrix models
> #4,-0.024812,-0.81188,0.5833,261.4,0.56239,-0.49373,-0.66328,258.68,0.8265,0.31159,0.46884,283.35
> fitmap #4 inMap #1
Fit molecule R11.pdb (#4) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 361 atoms
average map value = 3.595, steps = 120
shifted from previous position = 2.38
rotated from previous position = 43.1 degrees
atoms outside contour = 135, contour level = 3.2169
Position of R11.pdb (#4) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.48795136 -0.86403643 0.12387301 255.50564040
0.18197453 -0.03809856 -0.98256489 210.93634359
0.85369125 0.50198560 0.13864238 261.57928241
Axis 0.75850414 -0.37288739 0.53444032
Axis point 0.00000000 101.22190014 204.48913717
Rotation angle (degrees) 101.87354836
Shift along axis 254.94510046
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #!1 models
> hide #!1 models
> show #!2 models
> select clear
> select #14/A:292
22 atoms, 24 bonds, 1 residue, 1 model selected
> fitmap #14 inMap #2
Fit molecule combination (#14) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 7197 atoms
average map value = 5.834, steps = 164
shifted from previous position = 7.85
rotated from previous position = 18.1 degrees
atoms outside contour = 2657, contour level = 4.1986
Position of combination (#14) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
0.99999827 -0.00120444 -0.00142010 0.55228820
0.00120289 0.99999868 -0.00109052 -0.02352920
0.00142141 0.00108881 0.99999840 -0.53428451
Axis 0.50506202 -0.65852497 0.55790431
Axis point 374.89181466 0.00000000 389.74675539
Rotation angle (degrees) 0.12361471
Shift along axis -0.00364526
> show #!1 models
> select #2
2 models selected
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 4 atomic models, 2 maps.
> hide #3 models
> hide #!4 models
> hide #8 models
> hide #!14 models
> fitmap #2 inMap #1
Fit map cryosparc_P104_J81_mono_3dot25_map_emready.mrc in map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc using 49672 points
correlation = 0.8947, correlation about mean = 0.1823, overlap = 1.633e+06
steps = 144, shift = 7.63, angle = 17.1 degrees
Position of cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.47759429 0.87137073 0.11232427 132.33349948
-0.60130020 -0.23096860 -0.76491279 540.46786996
-0.64057923 -0.43285859 0.63426468 317.94477584
Axis 0.19683414 0.44630399 -0.87296567
Axis point 273.32095182 309.28022861 0.00000000
Rotation angle (degrees) 122.48977629
Shift along axis -10.29415761
> show #3 models
> show #!4 models
> show #8 models
> show #9 models
> hide #9 models
> show #!14 models
> select clear
> select #14/A:291
22 atoms, 24 bonds, 1 residue, 1 model selected
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 4 atomic models, 2 maps.
> hide #!1 models
> fitmap #14 inMap #2
Fit molecule combination (#14) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 7197 atoms
average map value = 5.834, steps = 160
shifted from previous position = 7.54
rotated from previous position = 17.1 degrees
atoms outside contour = 2655, contour level = 4.1986
Position of combination (#14) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
0.99999835 -0.00121205 -0.00135081 0.54654269
0.00121063 0.99999872 -0.00105018 -0.02865544
0.00135208 0.00104854 0.99999854 -0.50162697
Axis 0.50055278 -0.64464915 0.57781864
Axis point 372.38003937 0.00000000 403.33672698
Rotation angle (degrees) 0.12011492
Shift along axis 0.00219676
> show #!1 models
> show #9 models
> hide #!2 models
> hide #3 models
> hide #!4 models
> hide #8 models
> hide #9 models
> show #9 models
> show #8 models
> show #!4 models
> show #3 models
> hide #9 models
> show #9 models
> hide #9 models
> hide #3 models
> show #3 models
> hide #!4 models
> show #!4 models
> hide #8 models
> show #8 models
> hide #!14 models
> show #!14 models
> combine #3 #4 #8 #14
Remapping chain ID 'A' in R11.pdb #4 to 'B'
Remapping chain ID 'A' in fold_r_efa_model_0.cif #8 to 'C'
Remapping chain ID 'A' in combination #14 to 'I'
Remapping chain ID 'B' in combination #14 to 'J'
Remapping chain ID 'C' in combination #14 to 'K'
> hide #!14 models
> hide #8 models
> hide #!4 models
> hide #3 models
> hide #!5 models
> show #!5 models
> close #3#4
> show #8 models
> hide #!5 models
> close #8
> show #!14 models
> show #!5 models
> hide #!5 models
> close #14
> show #!5 models
> hide #!5 models
> show #9 models
> hide #!1 models
> select #9/A:519
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #9/A:518
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add #9/A:517
66 atoms, 71 bonds, 3 residues, 1 model selected
> select add #9/A:516
86 atoms, 92 bonds, 4 residues, 1 model selected
> select up
12448 atoms, 13961 bonds, 580 residues, 1 model selected
> cartoon hide sel
> cartoon sel
> hide sel target a
> select clear
> select #9/A:519
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #9/A:518
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add #9/A:517
66 atoms, 71 bonds, 3 residues, 1 model selected
> select add #9/A:516
86 atoms, 92 bonds, 4 residues, 1 model selected
> select add #9/A:515
108 atoms, 116 bonds, 5 residues, 1 model selected
> select add #9/A:514
128 atoms, 137 bonds, 6 residues, 1 model selected
> select add #9/A:513
151 atoms, 162 bonds, 7 residues, 1 model selected
> select add #9/A:512
174 atoms, 187 bonds, 8 residues, 1 model selected
> select add #9/A:432
197 atoms, 212 bonds, 9 residues, 1 model selected
> select add #9/A:433
217 atoms, 233 bonds, 10 residues, 1 model selected
> select add #9/A:434
237 atoms, 254 bonds, 11 residues, 1 model selected
> select add #9/A:435
259 atoms, 278 bonds, 12 residues, 1 model selected
> select add #9/A:436
279 atoms, 299 bonds, 13 residues, 1 model selected
> select add #9/A:437
299 atoms, 320 bonds, 14 residues, 1 model selected
> select add #9/A:438
321 atoms, 344 bonds, 15 residues, 1 model selected
> select add #9/A:439
344 atoms, 369 bonds, 16 residues, 1 model selected
> select add #9/A:440
364 atoms, 390 bonds, 17 residues, 1 model selected
> select add #9/A:441
384 atoms, 411 bonds, 18 residues, 1 model selected
> select add #9/A:442
406 atoms, 435 bonds, 19 residues, 1 model selected
> select add #9/A:443
429 atoms, 460 bonds, 20 residues, 1 model selected
> select add #9/A:444
449 atoms, 481 bonds, 21 residues, 1 model selected
> select add #9/A:445
471 atoms, 505 bonds, 22 residues, 1 model selected
> select add #9/A:446
494 atoms, 530 bonds, 23 residues, 1 model selected
> select add #9/A:447
516 atoms, 554 bonds, 24 residues, 1 model selected
> select add #9/A:448
539 atoms, 579 bonds, 25 residues, 1 model selected
> select add #9/A:449
559 atoms, 600 bonds, 26 residues, 1 model selected
> select add #9/A:450
579 atoms, 621 bonds, 27 residues, 1 model selected
> select add #9/A:451
601 atoms, 645 bonds, 28 residues, 1 model selected
> select add #9/A:452
624 atoms, 670 bonds, 29 residues, 1 model selected
> select add #9/A:453
646 atoms, 694 bonds, 30 residues, 1 model selected
> select add #9/A:454
666 atoms, 715 bonds, 31 residues, 1 model selected
> select add #9/A:455
686 atoms, 736 bonds, 32 residues, 1 model selected
> select add #9/A:456
708 atoms, 760 bonds, 33 residues, 1 model selected
> select add #9/A:457
728 atoms, 781 bonds, 34 residues, 1 model selected
> select add #9/A:458
750 atoms, 805 bonds, 35 residues, 1 model selected
> select add #9/A:459
770 atoms, 826 bonds, 36 residues, 1 model selected
> select add #9/A:460
792 atoms, 850 bonds, 37 residues, 1 model selected
> select add #9/A:461
815 atoms, 875 bonds, 38 residues, 1 model selected
> select add #9/A:462
837 atoms, 899 bonds, 39 residues, 1 model selected
> select add #9/A:463
859 atoms, 923 bonds, 40 residues, 1 model selected
> select add #9/A:465
881 atoms, 947 bonds, 41 residues, 1 model selected
> select add #9/A:464
903 atoms, 971 bonds, 42 residues, 1 model selected
> select add #9/A:466
925 atoms, 995 bonds, 43 residues, 1 model selected
> select add #9/A:467
948 atoms, 1020 bonds, 44 residues, 1 model selected
> select add #9/A:468
968 atoms, 1041 bonds, 45 residues, 1 model selected
> select add #9/A:469
990 atoms, 1065 bonds, 46 residues, 1 model selected
> select add #9/A:470
1012 atoms, 1089 bonds, 47 residues, 1 model selected
> select add #9/A:511
1035 atoms, 1114 bonds, 48 residues, 1 model selected
> select add #9/A:510
1055 atoms, 1135 bonds, 49 residues, 1 model selected
> select add #9/A:509
1075 atoms, 1156 bonds, 50 residues, 1 model selected
> select add #9/A:508
1095 atoms, 1177 bonds, 51 residues, 1 model selected
> select add #9/A:507
1115 atoms, 1198 bonds, 52 residues, 1 model selected
> select add #9/A:506
1135 atoms, 1219 bonds, 53 residues, 1 model selected
> select add #9/A:505
1155 atoms, 1240 bonds, 54 residues, 1 model selected
> select add #9/A:504
1175 atoms, 1261 bonds, 55 residues, 1 model selected
> select add #9/A:503
1198 atoms, 1286 bonds, 56 residues, 1 model selected
> select add #9/A:471
1220 atoms, 1310 bonds, 57 residues, 1 model selected
> select add #9/A:472
1243 atoms, 1335 bonds, 58 residues, 1 model selected
> select add #9/A:473
1265 atoms, 1359 bonds, 59 residues, 1 model selected
> select add #9/A:502
1287 atoms, 1383 bonds, 60 residues, 1 model selected
> select add #9/A:501
1307 atoms, 1404 bonds, 61 residues, 1 model selected
> select add #9/A:474
1330 atoms, 1429 bonds, 62 residues, 1 model selected
> select add #9/A:475
1352 atoms, 1453 bonds, 63 residues, 1 model selected
> select add #9/A:476
1374 atoms, 1477 bonds, 64 residues, 1 model selected
> select add #9/A:500
1394 atoms, 1498 bonds, 65 residues, 1 model selected
> select add #9/A:499
1414 atoms, 1519 bonds, 66 residues, 1 model selected
> select add #9/A:497
1436 atoms, 1543 bonds, 67 residues, 1 model selected
> select add #9/A:498
1459 atoms, 1568 bonds, 68 residues, 1 model selected
> select add #9/A:496
1479 atoms, 1589 bonds, 69 residues, 1 model selected
> select add #9/A:495
1501 atoms, 1613 bonds, 70 residues, 1 model selected
> select add #9/A:494
1524 atoms, 1638 bonds, 71 residues, 1 model selected
> select add #9/A:493
1544 atoms, 1659 bonds, 72 residues, 1 model selected
> select add #9/A:492
1564 atoms, 1680 bonds, 73 residues, 1 model selected
> select add #9/A:491
1584 atoms, 1701 bonds, 74 residues, 1 model selected
> select add #9/A:490
1607 atoms, 1726 bonds, 75 residues, 1 model selected
> select add #9/A:477
1630 atoms, 1751 bonds, 76 residues, 1 model selected
> select add #9/A:478
1650 atoms, 1772 bonds, 77 residues, 1 model selected
> select add #9/A:479
1670 atoms, 1793 bonds, 78 residues, 1 model selected
> select add #9/A:480
1692 atoms, 1817 bonds, 79 residues, 1 model selected
> select add #9/A:481
1712 atoms, 1838 bonds, 80 residues, 1 model selected
> select add #9/A:482
1732 atoms, 1859 bonds, 81 residues, 1 model selected
> select add #9/A:483
1755 atoms, 1884 bonds, 82 residues, 1 model selected
> select add #9/A:484
1778 atoms, 1909 bonds, 83 residues, 1 model selected
> select add #9/A:485
1801 atoms, 1934 bonds, 84 residues, 1 model selected
> select add #9/A:486
1821 atoms, 1955 bonds, 85 residues, 1 model selected
> select add #9/A:487
1843 atoms, 1979 bonds, 86 residues, 1 model selected
> select add #9/A:488
1866 atoms, 2004 bonds, 87 residues, 1 model selected
> select add #9/A:489
1886 atoms, 2025 bonds, 88 residues, 1 model selected
> select ~sel & ##selected
10562 atoms, 11849 bonds, 492 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!2 models
Drag select of 88 residues
> ui mousemode right "translate selected models"
> view matrix models #9,1,0,0,41.263,0,1,0,144.01,0,0,1,230.28
> view matrix models #9,1,0,0,219.74,0,1,0,136.11,0,0,1,249.41
> view matrix models #9,1,0,0,154.35,0,1,0,159.36,0,0,1,226.92
> view matrix models #9,1,0,0,181.32,0,1,0,233.48,0,0,1,173.65
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.32679,0.60574,-0.72546,218.6,-0.53288,-0.51586,-0.67077,286.3,-0.78054,0.60578,0.15421,218.01
> view matrix models
> #9,-0.88041,0.29197,-0.37367,238.37,-0.39531,-0.88712,0.23822,253.08,-0.26194,0.35745,0.89645,180.36
> view matrix models
> #9,-0.87581,0.46533,-0.12815,227.48,-0.45144,-0.69583,0.55859,240.75,0.17076,0.54707,0.81948,170.7
> view matrix models
> #9,-0.68046,0.28151,0.67656,194.83,0.032567,-0.91074,0.4117,236.41,0.73207,0.30218,0.61055,167.05
> view matrix models
> #9,-0.85807,0.45586,0.23647,213.7,-0.2549,-0.77781,0.57449,236.15,0.44581,0.43268,0.78361,166.4
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.85807,0.45586,0.23647,261.8,-0.2549,-0.77781,0.57449,145.88,0.44581,0.43268,0.78361,193.52
> view matrix models
> #9,-0.85807,0.45586,0.23647,262.78,-0.2549,-0.77781,0.57449,142.92,0.44581,0.43268,0.78361,193.07
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.55794,-0.37125,0.74221,217.55,0.19875,-0.80856,-0.55384,173.7,0.80573,0.45652,-0.37734,226.82
> view matrix models
> #9,0.98742,-0.13439,-0.083281,235.11,-0.14258,-0.52936,-0.83633,189.73,0.068309,0.83769,-0.54186,247.21
> view matrix models
> #9,0.6963,0.64033,-0.32426,243.47,-0.2113,-0.24888,-0.9452,192.66,-0.68594,0.72667,-0.03799,248.25
> view matrix models
> #9,0.99899,-0.04184,0.016596,230.22,0.002624,-0.31395,-0.94944,188.2,0.044935,0.94852,-0.31352,238.27
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.99899,-0.04184,0.016596,231.19,0.002624,-0.31395,-0.94944,184.33,0.044935,0.94852,-0.31352,248.01
> view matrix models
> #9,0.99899,-0.04184,0.016596,235.54,0.002624,-0.31395,-0.94944,195.82,0.044935,0.94852,-0.31352,238.21
> view matrix models
> #9,0.99899,-0.04184,0.016596,237.39,0.002624,-0.31395,-0.94944,194.14,0.044935,0.94852,-0.31352,243.33
> fitmap #9 inMap #2
Fit molecule fold_r_efa_model_0.cif (#9) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 1886 atoms
average map value = 2.442, steps = 600
shifted from previous position = 14.8
rotated from previous position = 32.4 degrees
atoms outside contour = 1442, contour level = 4.1986
Position of fold_r_efa_model_0.cif (#9) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
-0.36298980 -0.26180162 0.89425853 189.41512718
0.89898660 0.15402227 0.41000028 205.39844361
-0.24507446 0.95275235 0.17944764 240.11193695
Axis 0.31653466 0.66446246 0.67697522
Axis point 52.42370966 16.54185657 0.00000000
Rotation angle (degrees) 120.98141072
Shift along axis 358.98583936
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.86718,-0.44716,0.21918,247.48,0.029717,-0.39288,-0.91911,202.99,0.4971,0.80355,-0.32741,227.76
> view matrix models
> #9,0.86836,-0.44435,0.22024,247.38,0.033782,-0.39006,-0.92017,202.9,0.49478,0.80648,-0.3237,227.65
> view matrix models
> #9,0.58834,-0.19676,0.78431,231,0.68961,-0.38439,-0.61374,175.45,0.42224,0.90196,-0.090461,219.89
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.58834,-0.19676,0.78431,220.42,0.68961,-0.38439,-0.61374,172.67,0.42224,0.90196,-0.090461,231.53
> view matrix models
> #9,0.58834,-0.19676,0.78431,223.9,0.68961,-0.38439,-0.61374,162.31,0.42224,0.90196,-0.090461,233.05
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.72775,-0.4496,0.51792,232.8,0.21721,-0.56519,-0.79585,182.41,0.65054,0.69167,-0.31366,237.76
> view matrix models
> #9,0.79601,-0.22175,0.5632,227.2,0.38485,-0.53277,-0.75369,176.42,0.46719,0.81669,-0.33875,241.95
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.79601,-0.22175,0.5632,224.22,0.38485,-0.53277,-0.75369,181.42,0.46719,0.81669,-0.33875,243.13
> view matrix models
> #9,0.79601,-0.22175,0.5632,220.89,0.38485,-0.53277,-0.75369,180.86,0.46719,0.81669,-0.33875,242.55
> hide #!2 models
> fitmap #9 inMap #1
Fit molecule fold_r_efa_model_0.cif (#9) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 1886 atoms
average map value = 3.243, steps = 124
shifted from previous position = 6.38
rotated from previous position = 25.3 degrees
atoms outside contour = 845, contour level = 3.2169
Position of fold_r_efa_model_0.cif (#9) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.94619130 -0.27848943 0.16482009 236.29978662
0.00123308 -0.50621407 -0.86240697 196.35454887
0.32360547 0.81620521 -0.47863195 255.26678505
Axis 0.98213231 -0.09290309 0.16366169
Axis point 0.00000000 48.23674098 170.97141072
Rotation angle (degrees) 121.28714334
Shift along axis 255.61310470
> show #!2 models
> select clear
> select #9/A:459
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #9/A:458
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add #9/A:456
64 atoms, 69 bonds, 3 residues, 1 model selected
> select add #9/A:457
84 atoms, 90 bonds, 4 residues, 1 model selected
> select add #9/A:455
104 atoms, 111 bonds, 5 residues, 1 model selected
> select add #9/A:454
124 atoms, 132 bonds, 6 residues, 1 model selected
> select add #9/A:512
147 atoms, 157 bonds, 7 residues, 1 model selected
> select add #9/A:513
170 atoms, 182 bonds, 8 residues, 1 model selected
> select add #9/A:514
190 atoms, 203 bonds, 9 residues, 1 model selected
> select add #9/A:515
212 atoms, 227 bonds, 10 residues, 1 model selected
> select add #9/A:516
232 atoms, 248 bonds, 11 residues, 1 model selected
> select add #9/A:517
255 atoms, 273 bonds, 12 residues, 1 model selected
> select add #9/A:518
275 atoms, 294 bonds, 13 residues, 1 model selected
> select add #9/A:519
298 atoms, 319 bonds, 14 residues, 1 model selected
> select add #9/A:432
321 atoms, 344 bonds, 15 residues, 1 model selected
> select add #9/A:433
341 atoms, 365 bonds, 16 residues, 1 model selected
> select add #9/A:434
361 atoms, 386 bonds, 17 residues, 1 model selected
> select add #9/A:435
383 atoms, 410 bonds, 18 residues, 1 model selected
Drag select of 1 residues
> select #9/A:459
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #9/A:512
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add #9/A:458
65 atoms, 70 bonds, 3 residues, 1 model selected
> select add #9/A:457
85 atoms, 91 bonds, 4 residues, 1 model selected
> select add #9/A:456
107 atoms, 115 bonds, 5 residues, 1 model selected
> select add #9/A:455
127 atoms, 136 bonds, 6 residues, 1 model selected
> select add #9/A:454
147 atoms, 157 bonds, 7 residues, 1 model selected
> select add #9/A:513
170 atoms, 182 bonds, 8 residues, 1 model selected
> select add #9/A:514
190 atoms, 203 bonds, 9 residues, 1 model selected
> select add #9/A:515
212 atoms, 227 bonds, 10 residues, 1 model selected
> select add #9/A:516
232 atoms, 248 bonds, 11 residues, 1 model selected
> select add #9/A:517
255 atoms, 273 bonds, 12 residues, 1 model selected
> select add #9/A:518
275 atoms, 294 bonds, 13 residues, 1 model selected
> select add #9/A:519
298 atoms, 319 bonds, 14 residues, 1 model selected
> select add #9/A:453
320 atoms, 343 bonds, 15 residues, 1 model selected
> select add #9/A:452
343 atoms, 368 bonds, 16 residues, 1 model selected
> select add #9/A:451
365 atoms, 392 bonds, 17 residues, 1 model selected
> select add #9/A:450
385 atoms, 413 bonds, 18 residues, 1 model selected
> select add #9/A:449
405 atoms, 434 bonds, 19 residues, 1 model selected
> select add #9/A:448
428 atoms, 459 bonds, 20 residues, 1 model selected
> select add #9/A:447
450 atoms, 483 bonds, 21 residues, 1 model selected
> select add #9/A:446
473 atoms, 508 bonds, 22 residues, 1 model selected
> select add #9/A:445
495 atoms, 532 bonds, 23 residues, 1 model selected
> select add #9/A:444
515 atoms, 553 bonds, 24 residues, 1 model selected
> select add #9/A:443
538 atoms, 578 bonds, 25 residues, 1 model selected
> select add #9/A:442
560 atoms, 602 bonds, 26 residues, 1 model selected
> select add #9/A:441
580 atoms, 623 bonds, 27 residues, 1 model selected
> select add #9/A:440
600 atoms, 644 bonds, 28 residues, 1 model selected
> select add #9/A:439
623 atoms, 669 bonds, 29 residues, 1 model selected
> select add #9/A:438
645 atoms, 693 bonds, 30 residues, 1 model selected
> select add #9/A:437
665 atoms, 714 bonds, 31 residues, 1 model selected
> select add #9/A:436
685 atoms, 735 bonds, 32 residues, 1 model selected
> select add #9/A:435
707 atoms, 759 bonds, 33 residues, 1 model selected
> select add #9/A:434
727 atoms, 780 bonds, 34 residues, 1 model selected
> select add #9/A:433
747 atoms, 801 bonds, 35 residues, 1 model selected
> select add #9/A:432
770 atoms, 826 bonds, 36 residues, 1 model selected
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R12.pdb models #9
> selectedOnly true relModel #9
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R12.pdb
Chain information for R12.pdb #3
---
Chain | Description
A | No description available
> delete atoms sel
> delete bonds sel
> show #!2 models
> show #!1 models
Drag select of 1 shapes
> view matrix models #3,1,0,0,-50.191,0,1,0,37.877,0,0,1,225.97
> view matrix models #3,1,0,0,146.28,0,1,0,44.293,0,0,1,340.67
> view matrix models #3,1,0,0,215.82,0,1,0,215.09,0,0,1,268.85
> view matrix models #3,1,0,0,242.67,0,1,0,189.42,0,0,1,228.63
> view matrix models #3,1,0,0,253.2,0,1,0,189.42,0,0,1,204.72
> view matrix models #3,1,0,0,243.03,0,1,0,189.89,0,0,1,195.75
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.97525,0.10679,0.19359,238.96,-0.13692,0.97922,0.14958,186.6,-0.1736,-0.17239,0.96961,196.18
> hide #!2 models
> show #!2 models
> hide #!1 models
> fitmap #3 inMap #2
Fit molecule R12.pdb (#3) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 770 atoms
average map value = 3.607, steps = 92
shifted from previous position = 4.54
rotated from previous position = 20.1 degrees
atoms outside contour = 485, contour level = 4.1986
Position of R12.pdb (#3) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
-0.58257938 -0.39982764 -0.70762923 238.80442532
0.81079941 -0.22524337 -0.54024971 234.63448659
0.05661798 -0.88848370 0.45540216 205.91116344
Axis -0.23634444 -0.51869026 0.82164574
Axis point 87.50522764 245.61481572 0.00000000
Rotation angle (degrees) 132.54820723
Shift along axis -8.95669163
> view matrix models
> #3,0.99205,-0.10564,-0.06846,245.42,0.11794,0.97009,0.21215,184.84,0.044001,-0.21854,0.97484,194.09
> view matrix models
> #3,-0.049106,-0.75511,-0.65376,267.21,0.27118,-0.64004,0.71889,140.07,-0.96128,-0.14198,0.2362,232.28
> view matrix models
> #3,-0.67562,-0.72577,-0.12957,259.35,-0.020321,-0.15735,0.98733,143.38,-0.73697,0.6697,0.091557,247.31
> view matrix models
> #3,-0.40256,-0.54714,0.73388,231.17,0.63029,0.41572,0.65568,154.73,-0.66384,0.7265,0.17751,244.53
> view matrix models
> #3,-0.34003,-0.24602,0.90766,229.77,0.64004,0.6466,0.41503,166.08,-0.689,0.72207,-0.062405,252.43
> view matrix models
> #3,-0.41698,-0.44324,0.79351,231.18,0.50315,0.6145,0.60764,161.24,-0.75694,0.65264,-0.033218,251.26
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.41698,-0.44324,0.79351,235.03,0.50315,0.6145,0.60764,156.74,-0.75694,0.65264,-0.033218,248.36
> fitmap #3 inMap #2
Fit molecule R12.pdb (#3) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 770 atoms
average map value = 3.024, steps = 128
shifted from previous position = 3.57
rotated from previous position = 29.1 degrees
atoms outside contour = 523, contour level = 4.1986
Position of R12.pdb (#3) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
0.24518153 -0.87965383 -0.40754774 213.20447272
-0.48421084 -0.47530228 0.73459350 210.27644424
-0.83989635 0.01723028 -0.54247326 263.58066496
Axis -0.77449411 0.46678091 0.42693612
Axis point 0.00000000 208.08133390 160.59594891
Rotation angle (degrees) 152.41155621
Shift along axis 45.55952671
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.65874,0.012194,0.75227,244.44,0.57613,0.65123,0.49394,162.8,-0.48388,0.75878,-0.43602,258.34
> view matrix models
> #3,0.1747,0.015883,0.98449,225.99,0.95932,0.22248,-0.17382,171.88,-0.22179,0.97481,0.023629,243.78
> view matrix models
> #3,0.17745,0.48375,0.85703,237.75,0.37108,0.77368,-0.51354,199.65,-0.91149,0.40915,-0.042223,245.73
> view matrix models
> #3,0.54555,0.19148,0.81591,229.32,0.63362,0.54297,-0.55109,193.53,-0.54854,0.81763,0.1749,240.72
> view matrix models
> #3,0.30489,-0.24467,0.92042,222,0.68615,0.72666,-0.034125,179.4,-0.66049,0.64195,0.38943,232.48
> view matrix models
> #3,0.59993,-0.63039,0.49263,225.32,0.79887,0.43846,-0.41178,185.17,0.043581,0.64059,0.76665,211.06
> view matrix models
> #3,0.86021,0.36827,0.35273,242.8,0.060427,0.61323,-0.78759,209.86,-0.50635,0.69881,0.50525,227.67
> view matrix models
> #3,0.67543,0.036033,0.73654,227.55,0.33587,0.87416,-0.35076,196.59,-0.6565,0.4843,0.57833,223.8
> view matrix models
> #3,0.60004,-0.51561,0.61164,223.42,0.57331,0.8104,0.12071,177.36,-0.55791,0.27823,0.78188,212.6
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.60004,-0.51561,0.61164,216.61,0.57331,0.8104,0.12071,178.58,-0.55791,0.27823,0.78188,216.35
> view matrix models
> #3,0.60004,-0.51561,0.61164,220.1,0.57331,0.8104,0.12071,177.62,-0.55791,0.27823,0.78188,214.92
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.30366,-0.81599,0.49189,222.91,0.74882,0.52361,0.40633,161.45,-0.58912,0.24495,0.77003,215.16
> view matrix models
> #3,0.25986,-0.71236,0.65193,220.11,0.72633,0.58908,0.35417,164.49,-0.63633,0.38148,0.67049,221.22
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.25986,-0.71236,0.65193,219.91,0.72633,0.58908,0.35417,159.32,-0.63633,0.38148,0.67049,222.94
> view matrix models
> #3,0.25986,-0.71236,0.65193,221.11,0.72633,0.58908,0.35417,159.25,-0.63633,0.38148,0.67049,222.52
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.25971,-0.71353,0.65071,221.13,0.72729,0.58782,0.35429,159.21,-0.63529,0.38124,0.67161,222.47
> view matrix models
> #3,0.9098,-0.20228,0.36242,230.09,0.29964,0.92433,-0.23628,189.28,-0.2872,0.32357,0.90157,209.55
> view matrix models
> #3,0.92766,0.32309,-0.18723,256.04,-0.37245,0.83669,-0.40153,202.05,0.026921,0.44222,0.8965,207.49
> view matrix models
> #3,0.80355,-0.41296,-0.42869,253.22,-0.54927,-0.23689,-0.80136,199.41,0.22938,0.8794,-0.41718,253.85
> view matrix models
> #3,0.84689,0.09253,-0.52366,264.02,-0.2792,-0.76073,-0.58595,180.3,-0.45258,0.64244,-0.61841,265.43
> view matrix models
> #3,0.89594,-0.43708,0.079113,235.42,-0.43621,-0.89938,-0.028893,162.36,0.083781,-0.0086236,-0.99645,259.57
> view matrix models
> #3,-0.016224,-0.99263,0.12005,237.1,-0.93978,-0.025857,-0.3408,193.43,0.34139,-0.11835,-0.93244,252.28
> view matrix models
> #3,0.74139,-0.62719,0.23869,229.26,-0.44485,-0.72564,-0.52494,181.14,0.50244,0.283,-0.81699,253.09
> view matrix models
> #3,0.44957,-0.79213,0.41282,224.88,-0.71792,-0.59541,-0.36067,181.7,0.5315,-0.13423,-0.83636,246.43
> view matrix models
> #3,-0.037505,-0.87608,0.48071,227.82,-0.98212,-0.056494,-0.17958,188.36,0.18449,-0.47884,-0.8583,246.06
> view matrix models
> #3,-0.51017,-0.84925,-0.136,254.2,-0.48849,0.41626,-0.76688,208.29,0.70789,-0.3248,-0.62722,234.27
> view matrix models
> #3,-0.29987,-0.90587,0.29914,236.61,-0.55319,-0.090346,-0.82814,202.74,0.77721,-0.41381,-0.47403,226.99
> fitmap #3 inMap #2
Fit molecule R12.pdb (#3) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 770 atoms
average map value = 5.168, steps = 88
shifted from previous position = 6.9
rotated from previous position = 21.5 degrees
atoms outside contour = 310, contour level = 4.1986
Position of R12.pdb (#3) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
-0.31221035 0.70323993 0.63873179 210.20425143
-0.23945718 -0.70888502 0.66343220 205.67402676
0.91933941 0.05418149 0.38971709 212.69406482
Axis -0.52658665 -0.24253435 -0.81479052
Axis point 60.75190156 64.45747991 0.00000000
Rotation angle (degrees) 144.65555940
Shift along axis -333.87487593
> select #9/A:495
22 atoms, 24 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.94619,-0.27849,0.16482,238.22,0.0012331,-0.50621,-0.86241,200.13,0.32361,0.81621,-0.47863,242.64
> view matrix models
> #9,0.94619,-0.27849,0.16482,239.72,0.0012331,-0.50621,-0.86241,200.05,0.32361,0.81621,-0.47863,241.86
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 2 maps.
> hide #!2 models
> fitmap #9 inMap #1
Fit molecule fold_r_efa_model_0.cif (#9) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 1116 atoms
average map value = 2.507, steps = 100
shifted from previous position = 8.31
rotated from previous position = 18.4 degrees
atoms outside contour = 675, contour level = 3.2169
Position of fold_r_efa_model_0.cif (#9) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.98877804 -0.14910514 -0.00925415 237.73583242
-0.10825863 -0.67246622 -0.73216750 202.88810147
0.10294683 0.72495299 -0.68106175 264.98558628
Axis 0.99665927 -0.07674461 0.02793870
Axis point 0.00000000 54.22845804 177.21360245
Rotation angle (degrees) 133.02951147
Shift along axis 228.77440410
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.91467,-0.38337,0.12807,239.52,0.026187,-0.25998,-0.96526,199.27,0.40334,0.88625,-0.22775,233.87
> view matrix models
> #9,0.87884,-0.47512,-0.043533,249.94,-0.2349,-0.35146,-0.90626,205.98,0.41528,0.80668,-0.42048,243.61
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.87884,-0.47512,-0.043533,252.56,-0.2349,-0.35146,-0.90626,205.27,0.41528,0.80668,-0.42048,234.12
> view matrix models
> #9,0.87884,-0.47512,-0.043533,251.74,-0.2349,-0.35146,-0.90626,204.92,0.41528,0.80668,-0.42048,236.37
> fitmap #9 inMap #1
Fit molecule fold_r_efa_model_0.cif (#9) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 1116 atoms
average map value = 3.669, steps = 140
shifted from previous position = 11.9
rotated from previous position = 15.5 degrees
atoms outside contour = 387, contour level = 3.2169
Position of fold_r_efa_model_0.cif (#9) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.82641705 -0.48008627 -0.29419726 262.69845166
-0.47258351 -0.30735813 -0.82595145 204.49111848
0.30610404 0.82161314 -0.48088685 253.05237770
Axis 0.93956725 -0.34233768 0.00427865
Axis point 0.00000000 70.61600726 209.54351936
Rotation angle (degrees) 118.74511159
Shift along axis 177.90056805
> show #!5 models
> hide #!3 models
> show #!3 models
> combine #3 #5 #9
Remapping chain ID 'A' in combination #5 to 'L'
Remapping chain ID 'A' in fold_r_efa_model_0.cif #9 to 'M'
> hide #!4 models
> hide #!3 models
> hide #!5 models
> hide #9 models
> show #!5 models
> show #!4 models
> hide #!5 models
> close #5
> show #9 models
> hide #9 models
> hide #!4 models
> show #9 models
> close #9
> show #!3 models
> hide #!3 models
> close #3
> show #16 models
> hide #!2 models
> select #16/A:436
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #16/A:435
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add #16/A:434
62 atoms, 66 bonds, 3 residues, 1 model selected
> select add #16/A:433
82 atoms, 87 bonds, 4 residues, 1 model selected
> select add #16/A:432
105 atoms, 112 bonds, 5 residues, 1 model selected
> select add #16/A:431
127 atoms, 136 bonds, 6 residues, 1 model selected
> select add #16/A:343
150 atoms, 161 bonds, 7 residues, 1 model selected
> select add #16/A:344
173 atoms, 186 bonds, 8 residues, 1 model selected
> select add #16/A:345
193 atoms, 207 bonds, 9 residues, 1 model selected
> select add #16/A:346
215 atoms, 231 bonds, 10 residues, 1 model selected
> select add #16/A:347
235 atoms, 252 bonds, 11 residues, 1 model selected
> select add #16/A:348
258 atoms, 277 bonds, 12 residues, 1 model selected
> select add #16/A:349
280 atoms, 301 bonds, 13 residues, 1 model selected
> select add #16/A:350
303 atoms, 326 bonds, 14 residues, 1 model selected
> select add #16/A:350
303 atoms, 326 bonds, 14 residues, 1 model selected
> select add #16/A:351
323 atoms, 347 bonds, 15 residues, 1 model selected
> select add #16/A:352
345 atoms, 371 bonds, 16 residues, 1 model selected
> select add #16/A:353
368 atoms, 396 bonds, 17 residues, 1 model selected
> select add #16/A:430
390 atoms, 420 bonds, 18 residues, 1 model selected
> select add #16/A:429
412 atoms, 444 bonds, 19 residues, 1 model selected
> select add #16/A:428
435 atoms, 469 bonds, 20 residues, 1 model selected
> select add #16/A:427
455 atoms, 490 bonds, 21 residues, 1 model selected
> select add #16/A:426
478 atoms, 515 bonds, 22 residues, 1 model selected
> select add #16/A:425
500 atoms, 539 bonds, 23 residues, 1 model selected
> select add #16/A:424
522 atoms, 563 bonds, 24 residues, 1 model selected
> select add #16/A:423
542 atoms, 584 bonds, 25 residues, 1 model selected
> select add #16/A:422
562 atoms, 605 bonds, 26 residues, 1 model selected
> select add #16/A:354
582 atoms, 626 bonds, 27 residues, 1 model selected
> select add #16/A:355
602 atoms, 647 bonds, 28 residues, 1 model selected
> select add #16/A:356
622 atoms, 668 bonds, 29 residues, 1 model selected
> select add #16/A:357
644 atoms, 692 bonds, 30 residues, 1 model selected
> select add #16/A:358
666 atoms, 716 bonds, 31 residues, 1 model selected
> select add #16/A:359
686 atoms, 737 bonds, 32 residues, 1 model selected
> select add #16/A:360
709 atoms, 762 bonds, 33 residues, 1 model selected
> select add #16/A:361
729 atoms, 783 bonds, 34 residues, 1 model selected
> select add #16/A:362
751 atoms, 807 bonds, 35 residues, 1 model selected
> select add #16/A:363
774 atoms, 832 bonds, 36 residues, 1 model selected
> select add #16/A:364
794 atoms, 853 bonds, 37 residues, 1 model selected
> select add #16/A:421
814 atoms, 874 bonds, 38 residues, 1 model selected
> select add #16/A:420
837 atoms, 899 bonds, 39 residues, 1 model selected
> select add #16/A:418
859 atoms, 923 bonds, 40 residues, 1 model selected
> select add #16/A:419
879 atoms, 944 bonds, 41 residues, 1 model selected
> select add #16/A:417
901 atoms, 968 bonds, 42 residues, 1 model selected
> select add #16/A:416
924 atoms, 993 bonds, 43 residues, 1 model selected
> select add #16/A:415
944 atoms, 1014 bonds, 44 residues, 1 model selected
> select add #16/A:414
964 atoms, 1035 bonds, 45 residues, 1 model selected
> select add #16/A:365
986 atoms, 1059 bonds, 46 residues, 1 model selected
> select add #16/A:366
1008 atoms, 1083 bonds, 47 residues, 1 model selected
> select add #16/A:367
1028 atoms, 1104 bonds, 48 residues, 1 model selected
> select add #16/A:368
1048 atoms, 1125 bonds, 49 residues, 1 model selected
> select add #16/A:369
1068 atoms, 1146 bonds, 50 residues, 1 model selected
> select add #16/A:370
1090 atoms, 1170 bonds, 51 residues, 1 model selected
> select add #16/A:371
1110 atoms, 1191 bonds, 52 residues, 1 model selected
> select add #16/A:413
1133 atoms, 1216 bonds, 53 residues, 1 model selected
> select add #16/A:412
1153 atoms, 1237 bonds, 54 residues, 1 model selected
> select add #16/A:411
1175 atoms, 1261 bonds, 55 residues, 1 model selected
> select add #16/A:410
1197 atoms, 1285 bonds, 56 residues, 1 model selected
> select add #16/A:409
1219 atoms, 1309 bonds, 57 residues, 1 model selected
> select add #16/A:408
1239 atoms, 1330 bonds, 58 residues, 1 model selected
> select add #16/A:407
1262 atoms, 1355 bonds, 59 residues, 1 model selected
> select add #16/A:406
1282 atoms, 1376 bonds, 60 residues, 1 model selected
> select add #16/A:405
1304 atoms, 1400 bonds, 61 residues, 1 model selected
> select add #16/A:372
1324 atoms, 1421 bonds, 62 residues, 1 model selected
> select add #16/A:373
1344 atoms, 1442 bonds, 63 residues, 1 model selected
> select add #16/A:374
1366 atoms, 1466 bonds, 64 residues, 1 model selected
> select add #16/A:375
1386 atoms, 1487 bonds, 65 residues, 1 model selected
> select add #16/A:376
1408 atoms, 1511 bonds, 66 residues, 1 model selected
> select add #16/A:377
1431 atoms, 1536 bonds, 67 residues, 1 model selected
> select add #16/A:378
1453 atoms, 1560 bonds, 68 residues, 1 model selected
> select add #16/A:379
1473 atoms, 1581 bonds, 69 residues, 1 model selected
> select add #16/A:380
1496 atoms, 1606 bonds, 70 residues, 1 model selected
> select add #16/A:381
1518 atoms, 1630 bonds, 71 residues, 1 model selected
> select add #16/A:382
1538 atoms, 1651 bonds, 72 residues, 1 model selected
> select add #16/A:383
1560 atoms, 1675 bonds, 73 residues, 1 model selected
> select add #16/A:404
1580 atoms, 1696 bonds, 74 residues, 1 model selected
> select add #16/A:403
1600 atoms, 1717 bonds, 75 residues, 1 model selected
> select add #16/A:402
1620 atoms, 1738 bonds, 76 residues, 1 model selected
> select add #16/A:401
1640 atoms, 1759 bonds, 77 residues, 1 model selected
> select add #16/A:400
1660 atoms, 1780 bonds, 78 residues, 1 model selected
> select add #16/A:399
1682 atoms, 1804 bonds, 79 residues, 1 model selected
> select add #16/A:398
1705 atoms, 1829 bonds, 80 residues, 1 model selected
> select add #16/A:397
1728 atoms, 1854 bonds, 81 residues, 1 model selected
> select add #16/A:396
1751 atoms, 1879 bonds, 82 residues, 1 model selected
> select add #16/A:395
1771 atoms, 1900 bonds, 83 residues, 1 model selected
> select add #16/A:394
1793 atoms, 1924 bonds, 84 residues, 1 model selected
> select add #16/A:393
1815 atoms, 1948 bonds, 85 residues, 1 model selected
> select add #16/A:392
1837 atoms, 1972 bonds, 86 residues, 1 model selected
> select add #16/A:391
1859 atoms, 1996 bonds, 87 residues, 1 model selected
> select add #16/A:390
1881 atoms, 2020 bonds, 88 residues, 1 model selected
> select add #16/A:389
1901 atoms, 2041 bonds, 89 residues, 1 model selected
> select add #16/A:388
1923 atoms, 2065 bonds, 90 residues, 1 model selected
> select add #16/A:387
1945 atoms, 2089 bonds, 91 residues, 1 model selected
> select add #16/A:386
1965 atoms, 2110 bonds, 92 residues, 1 model selected
> select add #16/A:385
1987 atoms, 2134 bonds, 93 residues, 1 model selected
> select add #16/A:384
2009 atoms, 2158 bonds, 94 residues, 1 model selected
> select ~sel & ##selected
10439 atoms, 11710 bonds, 486 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!2 models
> show #!1 models
> hide #!1 models
Drag select of 42 residues, 82 shapes
> view matrix models #16,1,0,0,239.26,0,1,0,193.36,0,0,1,158.73
> ui mousemode right "rotate selected models"
> view matrix models
> #16,0.82142,-0.34682,-0.45275,274.14,-0.14781,0.63726,-0.75634,237.98,0.55084,0.6882,0.47219,130.5
> view matrix models
> #16,0.64755,-0.69391,-0.31491,289.96,0.06244,0.46018,-0.88563,245.9,0.75946,0.55383,0.34132,136.46
> ui mousemode right "translate selected models"
> view matrix models
> #16,0.64755,-0.69391,-0.31491,257.81,0.06244,0.46018,-0.88563,171.38,0.75946,0.55383,0.34132,226.11
> ui mousemode right "rotate selected models"
> view matrix models
> #16,0.98678,-0.11358,-0.11557,216.48,0.068376,0.93847,-0.33853,131.19,0.14691,0.32615,0.93383,231.64
> view matrix models
> #16,0.67569,0.19351,-0.71134,227.33,-0.67905,0.53896,-0.49841,171.68,0.28694,0.8198,0.49557,218.8
> view matrix models
> #16,0.97442,-0.1193,-0.19044,219.27,-0.079692,0.60893,-0.78921,164.56,0.21012,0.7842,0.58385,219.37
> view matrix models
> #16,0.62818,-0.62856,0.45859,230.5,0.75222,0.33995,-0.56444,152.35,0.19888,0.69953,0.68637,220.43
> view matrix models
> #16,-0.04727,-0.69298,0.71941,240.08,0.99791,-0.064584,0.0033573,148.34,0.044136,0.71806,0.69458,222.65
> view matrix models
> #16,0.051124,-0.95987,0.27575,264.74,0.8362,-0.10982,-0.53732,171.16,0.54604,0.25805,0.79703,230.41
> view matrix models
> #16,-0.032207,-0.89801,0.4388,258.43,0.97887,-0.11705,-0.16769,156.66,0.20195,0.42413,0.8828,227.25
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.032207,-0.89801,0.4388,271.7,0.97887,-0.11705,-0.16769,178.4,0.20195,0.42413,0.8828,232.19
> view matrix models
> #16,-0.032207,-0.89801,0.4388,279.48,0.97887,-0.11705,-0.16769,175.4,0.20195,0.42413,0.8828,232.96
> view matrix models
> #16,-0.032207,-0.89801,0.4388,279.97,0.97887,-0.11705,-0.16769,174.68,0.20195,0.42413,0.8828,233.54
> view matrix models
> #16,-0.032207,-0.89801,0.4388,281.76,0.97887,-0.11705,-0.16769,176.48,0.20195,0.42413,0.8828,236.15
> fitmap #16 inMap #2
Fit molecule fold_r_efa_model_4.cif (#16) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 2009 atoms
average map value = 2.45, steps = 332
shifted from previous position = 15.2
rotated from previous position = 18 degrees
atoms outside contour = 1513, contour level = 4.1986
Position of fold_r_efa_model_4.cif (#16) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
-0.85387889 0.28884792 -0.43296387 203.23398994
-0.38173167 -0.91303095 0.14371991 258.33021238
-0.35379622 0.28799542 0.88988026 229.56149618
Axis 0.20895018 -0.11465629 -0.97118163
Axis point 147.78960124 92.95460295 0.00000000
Rotation angle (degrees) 159.80361279
Shift along axis -210.09931383
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #16,0.035438,-0.90119,0.43197,280.31,0.87223,-0.18309,-0.45353,182.15,0.48781,0.39285,0.77956,236.01
> ui mousemode right "rotate selected models"
> view matrix models
> #16,0.96287,-0.16386,0.21456,231.8,0.26579,0.43588,-0.85986,178.5,0.047371,0.88496,0.46325,232.14
> view matrix models
> #16,0.97636,-0.039561,0.21252,225.68,0.1942,0.59239,-0.7819,170.12,-0.094962,0.80468,0.58607,235.13
> ui mousemode right "translate selected models"
> view matrix models
> #16,0.97636,-0.039561,0.21252,241.05,0.1942,0.59239,-0.7819,160.97,-0.094962,0.80468,0.58607,232.24
> view matrix models
> #16,0.97636,-0.039561,0.21252,239.09,0.1942,0.59239,-0.7819,153.84,-0.094962,0.80468,0.58607,227.71
> ui mousemode right "rotate selected models"
> view matrix models
> #16,0.99957,0.029211,-0.00019132,242.07,-0.014782,0.50014,-0.86582,165.39,-0.025196,0.86545,0.50036,226.02
> view matrix models
> #16,0.99914,-0.0013987,0.041338,242.21,0.036869,0.48314,-0.87477,165.35,-0.018749,0.87554,0.48278,225.95
> ui mousemode right "translate selected models"
> view matrix models
> #16,0.99914,-0.0013987,0.041338,239.13,0.036869,0.48314,-0.87477,156.8,-0.018749,0.87554,0.48278,219.39
> view matrix models
> #16,0.99914,-0.0013987,0.041338,238.33,0.036869,0.48314,-0.87477,158.77,-0.018749,0.87554,0.48278,224.31
> fitmap #16 inMap #2
Fit molecule fold_r_efa_model_4.cif (#16) to map
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) using 2009 atoms
average map value = 1.777, steps = 1576
shifted from previous position = 13.3
rotated from previous position = 22.4 degrees
atoms outside contour = 1615, contour level = 4.1986
Position of fold_r_efa_model_4.cif (#16) relative to
cryosparc_P104_J81_mono_3dot25_map_emready.mrc (#2) coordinates:
Matrix rotation and translation
-0.29211392 -0.80850120 0.51087697 236.54952839
0.95121881 -0.30105129 0.06746032 210.93904096
0.09925843 0.50566188 0.85700282 234.47612534
Axis 0.23564452 0.22134940 0.94629599
Axis point 39.11074645 135.54778532 0.00000000
Rotation angle (degrees) 111.59732832
Shift along axis 324.31664900
> show #!4 models
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/fold_r_efa/fold_r_efa_model_0.cif
Chain information for fold_r_efa_model_0.cif #3
---
Chain | Description
A | .
> hide #!2 models
> hide #3 models
> hide #!4 models
> show #3 models
> hide #16 models
> select #3/A:82
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
12448 atoms, 13961 bonds, 580 residues, 1 model selected
> hide sel target a
> select clear
> select #3/A:316
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #3/A:315
45 atoms, 49 bonds, 2 residues, 1 model selected
> select add #3/A:314
65 atoms, 70 bonds, 3 residues, 1 model selected
> select add #3/A:317
88 atoms, 95 bonds, 4 residues, 1 model selected
> select add #3/A:318
110 atoms, 119 bonds, 5 residues, 1 model selected
> select add #3/A:319
132 atoms, 143 bonds, 6 residues, 1 model selected
> select add #3/A:320
154 atoms, 167 bonds, 7 residues, 1 model selected
> select add #3/A:321
174 atoms, 188 bonds, 8 residues, 1 model selected
> select add #3/A:322
194 atoms, 209 bonds, 9 residues, 1 model selected
> select add #3/A:323
216 atoms, 233 bonds, 10 residues, 1 model selected
> select add #3/A:324
239 atoms, 258 bonds, 11 residues, 1 model selected
> select add #3/A:325
259 atoms, 279 bonds, 12 residues, 1 model selected
> select add #3/A:326
282 atoms, 304 bonds, 13 residues, 1 model selected
> select add #3/A:327
302 atoms, 325 bonds, 14 residues, 1 model selected
> select add #3/A:313
322 atoms, 346 bonds, 15 residues, 1 model selected
> select add #3/A:312
344 atoms, 370 bonds, 16 residues, 1 model selected
> select add #3/A:311
366 atoms, 394 bonds, 17 residues, 1 model selected
> select add #3/A:310
388 atoms, 418 bonds, 18 residues, 1 model selected
> select add #3/A:309
411 atoms, 443 bonds, 19 residues, 1 model selected
> select add #3/A:308
433 atoms, 467 bonds, 20 residues, 1 model selected
> select add #3/A:307
456 atoms, 492 bonds, 21 residues, 1 model selected
> select add #3/A:306
478 atoms, 516 bonds, 22 residues, 1 model selected
> select add #3/A:305
498 atoms, 537 bonds, 23 residues, 1 model selected
> select add #3/A:304
521 atoms, 562 bonds, 24 residues, 1 model selected
> select add #3/A:328
541 atoms, 583 bonds, 25 residues, 1 model selected
> select add #3/A:329
561 atoms, 604 bonds, 26 residues, 1 model selected
> select add #3/A:330
583 atoms, 628 bonds, 27 residues, 1 model selected
> select add #3/A:331
605 atoms, 652 bonds, 28 residues, 1 model selected
> select add #3/A:303
625 atoms, 673 bonds, 29 residues, 1 model selected
> select add #3/A:302
645 atoms, 694 bonds, 30 residues, 1 model selected
> select add #3/A:332
665 atoms, 715 bonds, 31 residues, 1 model selected
> select ~sel & ##selected
11783 atoms, 13216 bonds, 549 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!1 models
> show #!2 models
Drag select of 31 residues
> view matrix models #3,1,0,0,425.43,0,1,0,261.92,0,0,1,184.97
> view matrix models #3,1,0,0,263.73,0,1,0,204.67,0,0,1,172.86
> view matrix models #3,1,0,0,234.96,0,1,0,208.24,0,0,1,260.94
> hide #!2 models
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.95007,0.12676,-0.28513,237.04,0.25787,0.19555,0.94618,203.18,0.1757,-0.97247,0.15309,273.49
> view matrix models
> #3,0.98818,0.021358,-0.1518,236.21,0.13976,0.28134,0.94938,204.7,0.062983,-0.95937,0.27503,274.65
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.98818,0.021358,-0.1518,236.44,0.13976,0.28134,0.94938,204.11,0.062983,-0.95937,0.27503,268.22
> view matrix models
> #3,0.98818,0.021358,-0.1518,235.79,0.13976,0.28134,0.94938,202.04,0.062983,-0.95937,0.27503,271.25
> view matrix models
> #3,0.98818,0.021358,-0.1518,232.75,0.13976,0.28134,0.94938,199.89,0.062983,-0.95937,0.27503,271.76
> view matrix models
> #3,0.98818,0.021358,-0.1518,231.61,0.13976,0.28134,0.94938,197.24,0.062983,-0.95937,0.27503,267.58
> view matrix models
> #3,0.98818,0.021358,-0.1518,231.54,0.13976,0.28134,0.94938,195.82,0.062983,-0.95937,0.27503,269.63
> view matrix models
> #3,0.98818,0.021358,-0.1518,230.54,0.13976,0.28134,0.94938,196.01,0.062983,-0.95937,0.27503,269.38
> show #!4 models
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.9814,-0.19071,-0.021936,231.67,0.19156,0.98031,0.047832,195.51,0.012382,-0.051144,0.99861,255.91
> view matrix models
> #3,0.89146,-0.40623,-0.20071,236.97,0.30006,0.86118,-0.41028,198.14,0.33951,0.30552,0.8896,246.81
> view matrix models
> #3,0.83044,-0.55618,-0.032333,238.28,0.50696,0.77846,-0.37013,194.45,0.23103,0.29097,0.92842,248.81
> view matrix models
> #3,0.73859,-0.67207,0.053017,240.55,0.45709,0.44141,-0.77216,201.89,0.49554,0.59454,0.63321,242.96
> view matrix models
> #3,0.55968,-0.81236,0.16383,244.6,0.30112,0.015164,-0.95347,210.56,0.77207,0.58296,0.2531,240.56
> view matrix models
> #3,0.52214,-0.8343,0.17698,245.45,0.29761,-0.016234,-0.95455,210.94,0.79925,0.55107,0.23982,240.43
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.52214,-0.8343,0.17698,247.06,0.29761,-0.016234,-0.95455,199.79,0.79925,0.55107,0.23982,245.71
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.46115,-0.74271,0.48551,244.94,0.88307,0.33064,-0.33297,179.74,0.086766,0.58229,0.80834,255.17
> view matrix models
> #3,0.40622,-0.62472,0.66686,243.46,0.80782,-0.095581,-0.58163,187.32,0.4271,0.77497,0.46584,249.23
> view matrix models
> #3,0.43377,-0.59001,0.68098,242.46,0.79212,-0.11047,-0.60028,187.92,0.4294,0.7998,0.41944,249.32
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.43377,-0.59001,0.68098,248.87,0.79212,-0.11047,-0.60028,200.85,0.4294,0.7998,0.41944,245.94
> view matrix models
> #3,0.43377,-0.59001,0.68098,248.18,0.79212,-0.11047,-0.60028,202.57,0.4294,0.7998,0.41944,247.23
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.041019,-0.9732,0.22626,263.37,0.56198,-0.16477,-0.81057,209.39,0.82613,0.16041,0.54016,244.4
> view matrix models
> #3,0.10041,-0.93943,0.32771,261.04,0.54523,-0.22357,-0.80793,210.27,0.83225,0.2598,0.48975,243.74
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.10041,-0.93943,0.32771,259.33,0.54523,-0.22357,-0.80793,209.62,0.83225,0.2598,0.48975,242.28
> view matrix models
> #3,0.10041,-0.93943,0.32771,249.88,0.54523,-0.22357,-0.80793,205.14,0.83225,0.2598,0.48975,253.56
> select #3/A:332
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #3/A:331
42 atoms, 45 bonds, 2 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #3/A:302
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #3/A:303
40 atoms, 42 bonds, 2 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #3/A:308
22 atoms, 24 bonds, 1 residue, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.69992,-0.71388,-0.022168,236.39,0.63159,0.63314,-0.44746,191.99,0.33346,0.29918,0.89403,261.7
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.69992,-0.71388,-0.022168,242.2,0.63159,0.63314,-0.44746,194.31,0.33346,0.29918,0.89403,252.7
> view matrix models
> #3,0.69992,-0.71388,-0.022168,240.42,0.63159,0.63314,-0.44746,190.6,0.33346,0.29918,0.89403,250.33
> view matrix models
> #3,0.69992,-0.71388,-0.022168,239.48,0.63159,0.63314,-0.44746,186.69,0.33346,0.29918,0.89403,252.53
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.80906,-0.56013,0.17796,233.81,0.58383,0.7312,-0.35282,186.11,0.067498,0.38935,0.91861,257.76
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.80906,-0.56013,0.17796,235.82,0.58383,0.7312,-0.35282,192.73,0.067498,0.38935,0.91861,252.36
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.80906,-0.56013,0.17796,235.24,0.58383,0.7312,-0.35282,189.3,0.067498,0.38935,0.91861,254.84
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.52206,-0.83489,0.17439,244.68,0.81629,0.42983,-0.38591,186.96,0.24723,0.34382,0.90591,251.13
> view matrix models
> #3,0.53846,-0.84262,0.0067461,245.72,0.76916,0.48822,-0.41236,187.73,0.34417,0.22723,0.91099,249.91
> view matrix models
> #3,0.6939,-0.71988,0.016399,240.8,0.60895,0.57451,-0.54692,191.78,0.3843,0.3895,0.83702,248.01
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.6939,-0.71988,0.016399,237.47,0.60895,0.57451,-0.54692,188.21,0.3843,0.3895,0.83702,249.52
> view matrix models
> #3,0.6939,-0.71988,0.016399,239.83,0.60895,0.57451,-0.54692,188.39,0.3843,0.3895,0.83702,252.79
> view matrix models
> #3,0.6939,-0.71988,0.016399,240.74,0.60895,0.57451,-0.54692,188.11,0.3843,0.3895,0.83702,255.07
> show #16 models
> combine #3 #4 #16
Remapping chain ID 'A' in combination #4 to 'N'
Remapping chain ID 'A' in fold_r_efa_model_4.cif #16 to 'O'
> hide #!4 models
> hide #3 models
> hide #16 models
> hide #!5 models
> show #!5 models
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R13.pdb models #5 relModel #2
> hide #!5 models
> show #!5 models
> show #16 models
> hide #16 models
> view matrix models
> #3,0.6939,-0.71988,0.016399,282.23,0.60895,0.57451,-0.54692,160.01,0.3843,0.3895,0.83702,256.29
> view matrix models
> #3,0.6939,-0.71988,0.016399,281.69,0.60895,0.57451,-0.54692,160.36,0.3843,0.3895,0.83702,256.01
> view matrix models
> #3,0.6939,-0.71988,0.016399,285.44,0.60895,0.57451,-0.54692,156.69,0.3843,0.3895,0.83702,255.17
> select #5/O:417
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #5/O:416
45 atoms, 49 bonds, 2 residues, 1 model selected
> select add #5/O:415
65 atoms, 70 bonds, 3 residues, 1 model selected
> select add #5/O:414
85 atoms, 92 bonds, 4 residues, 1 model selected
> view matrix models
> #5,0.6939,-0.71988,0.016399,248.88,0.60895,0.57451,-0.54692,179.8,0.3843,0.3895,0.83702,256.2
> select add #5/O:364
105 atoms, 113 bonds, 5 residues, 1 model selected
> select add #5/O:365
127 atoms, 137 bonds, 6 residues, 1 model selected
> select add #5/O:366
149 atoms, 161 bonds, 7 residues, 1 model selected
> select add #5/O:367
169 atoms, 182 bonds, 8 residues, 1 model selected
> select add #5/O:369
189 atoms, 203 bonds, 9 residues, 1 model selected
> select add #5/O:368
209 atoms, 224 bonds, 10 residues, 1 model selected
> select add #5/O:370
231 atoms, 248 bonds, 11 residues, 1 model selected
> select add #5/O:371
251 atoms, 269 bonds, 12 residues, 1 model selected
> select add #5/O:372
271 atoms, 290 bonds, 13 residues, 1 model selected
> select add #5/O:413
294 atoms, 314 bonds, 14 residues, 1 model selected
> select add #5/O:412
314 atoms, 335 bonds, 15 residues, 1 model selected
> select add #5/O:411
336 atoms, 359 bonds, 16 residues, 1 model selected
> select add #5/O:410
358 atoms, 383 bonds, 17 residues, 1 model selected
> select add #5/O:409
380 atoms, 407 bonds, 18 residues, 1 model selected
> select add #5/O:408
400 atoms, 428 bonds, 19 residues, 1 model selected
> select add #5/O:373
420 atoms, 449 bonds, 20 residues, 1 model selected
> select add #5/O:407
443 atoms, 474 bonds, 21 residues, 1 model selected
> view matrix models
> #5,0.6939,-0.71988,0.016399,237.22,0.60895,0.57451,-0.54692,189.07,0.3843,0.3895,0.83702,237.3
> select add #5/O:374
465 atoms, 498 bonds, 22 residues, 1 model selected
> select add #5/O:375
485 atoms, 519 bonds, 23 residues, 1 model selected
> select add #5/O:376
507 atoms, 543 bonds, 24 residues, 1 model selected
> select add #5/O:377
530 atoms, 568 bonds, 25 residues, 1 model selected
> select add #5/O:378
552 atoms, 592 bonds, 26 residues, 1 model selected
> select add #5/O:406
572 atoms, 613 bonds, 27 residues, 1 model selected
> select add #5/O:405
594 atoms, 637 bonds, 28 residues, 1 model selected
> select add #5/O:404
614 atoms, 658 bonds, 29 residues, 1 model selected
> select add #5/O:403
634 atoms, 679 bonds, 30 residues, 1 model selected
> select add #5/O:402
654 atoms, 700 bonds, 31 residues, 1 model selected
> select add #5/O:401
674 atoms, 721 bonds, 32 residues, 1 model selected
> select add #5/O:400
694 atoms, 742 bonds, 33 residues, 1 model selected
> select add #5/O:399
716 atoms, 766 bonds, 34 residues, 1 model selected
> select add #5/O:379
736 atoms, 787 bonds, 35 residues, 1 model selected
> select add #5/O:380
759 atoms, 812 bonds, 36 residues, 1 model selected
> select add #5/O:381
781 atoms, 836 bonds, 37 residues, 1 model selected
> select add #5/O:398
804 atoms, 861 bonds, 38 residues, 1 model selected
> select add #5/O:382
824 atoms, 882 bonds, 39 residues, 1 model selected
> select add #5/O:383
846 atoms, 906 bonds, 40 residues, 1 model selected
> select add #5/O:384
868 atoms, 930 bonds, 41 residues, 1 model selected
> select add #5/O:385
890 atoms, 954 bonds, 42 residues, 1 model selected
> select add #5/O:386
910 atoms, 975 bonds, 43 residues, 1 model selected
> select add #5/O:387
932 atoms, 999 bonds, 44 residues, 1 model selected
> select add #5/O:388
954 atoms, 1023 bonds, 45 residues, 1 model selected
> select add #5/O:389
974 atoms, 1044 bonds, 46 residues, 1 model selected
> select add #5/O:390
996 atoms, 1068 bonds, 47 residues, 1 model selected
> select add #5/O:391
1018 atoms, 1092 bonds, 48 residues, 1 model selected
> select add #5/O:392
1040 atoms, 1116 bonds, 49 residues, 1 model selected
> select add #5/O:393
1062 atoms, 1140 bonds, 50 residues, 1 model selected
> select add #5/O:394
1084 atoms, 1164 bonds, 51 residues, 1 model selected
> 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
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