Opened 4 months ago

Last modified 4 months ago

#18814 closed defect

ChimeraX bug report submission — at Initial Version

Reported by: chimerax-bug-report@… Owned by:
Priority: normal Milestone:
Component: Window Toolkit Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault

Current thread 0x00000001fcfbe0c0 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, PIL._imagingmath, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, chimerax.segment._segment, chimerax.pdb._pdbio, chimerax.graphics._graphics, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 65)


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  "procRole" : "Foreground",
  "version" : 2,
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  "captureTime" : "2025-09-17 17:35:49.6749 -0400",
  "codeSigningMonitor" : 1,
  "incident" : "AD35C0FE-DAB9-479D-A87A-A89971198D7E",
  "pid" : 73888,
  "translated" : false,
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  "procLaunch" : "2025-09-16 16:53:41.9199 -0400",
  "procStartAbsTime" : 138562020478,
  "procExitAbsTime" : 880534076593,
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  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "codeSigningAuxiliaryInfo" : 0,
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===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3985_00049_volume_series/J3985_class_01_00049_volume.mrc

Opened J3985_class_01_00049_volume.mrc as #1, grid size 128,128,128, pixel
2.74, shown at level 0.0714, step 1, values float32  

> open
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3985_00049_volume_series/J3985_class_00_00049_volume.mrc

Opened J3985_class_00_00049_volume.mrc as #2, grid size 128,128,128, pixel
2.74, shown at level 0.0704, step 1, values float32  

> volume #2 level 0.1464

> volume #2 level 0.1878

> volume #1 level 0.1749

> volume #1 level 0.2362

> volume #2 level 0.2672

> volume #1 level 0.2324

> volume #1 level 0.2937

> volume #1 level 0.1634

> volume #1 level 0.1979

> volume #2 level 0.2879

> volume #1 level 0.2247

> volume #1 level 0.2055

> volume #2 level 0.3432

> volume #1 level 0.3014

> volume #1 level 0.1557

> ui tool show "Segment Map"

Select a density map in the Segment map field  
Segmenting J3985_class_01_00049_volume.mrc, density threshold 0.155709  
Showing 1 region surfaces  
187 watershed regions, grouped to 1 regions  
Showing J3985_class_01_00049_volume.seg - 1 regions, 1 surfaces  
Ungrouped to 3 regions  

> select #3.3

1 model selected  
Ungrouped to 8 regions  

> select #3.6

1 model selected  
Ungrouped to 5 regions  

> select #3.3

1 model selected  

> select add #3.14

2 models selected  

> select add #3.9

3 models selected  
Grouped 3 regions  
Ungrouped to 3 regions  

> select #3.6

1 model selected  
Ungrouped to 3 regions  

> select #3.3

1 model selected  
Ungrouped to 15 regions  

> select #3.31

1 model selected  

> select add #3.9

2 models selected  

> select add #3.14

3 models selected  
Grouped 3 regions  
Saving 1 regions to mrc file...  
Opened J3985_class_01_00049_volume_region_234.mrc as #4, grid size 21,17,18,
pixel 2.74, shown at step 1, values float32  
Wrote J3985_class_01_00049_volume_region_234.mrc  

> volume resample #4 onGrid 1

Invalid "onGrid" argument: invalid density maps specifier  

> volume resample #4 onGrid #1

Opened J3985_class_01_00049_volume_region_234.mrc resampled as #5, grid size
128,128,128, pixel 2.74, shown at step 1, values float32  

> hide #!3 models

> volume #5 level 0.2124

> volume #5 level 0.1251

> save
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3985_00049_volume_series/J3985_class_01_00049_volume_region_p.mrc
> models #5

> open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3986_006_volume_map.mrc

Opened cryosparc_P9_J3986_006_volume_map.mrc as #6, grid size 480,480,480,
pixel 0.732, shown at level 0.0101, step 2, values float32  

> volume #6 level 0.0249

> volume #6 level 0.01868

> volume #6 level 0.03345

> volume #!5-6 hide

> volume #1 level 0.2702

> volume #2 level 0.1264

> volume #1 level 0.1478

> volume #1 level 0.1123

> volume #2 level 0.1797

> volume #1 level 0.2623

> volume #2 level 0.3574

> volume #1 level 0.3294

> open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3984_007_volume_map.mrc

Opened cryosparc_P9_J3984_007_volume_map.mrc as #7, grid size 480,480,480,
pixel 0.732, shown at level 0.0104, step 2, values float32  

> volume #!1,7 hide

> volume #7 level 0.02771

> volume #7 level 0.04405

> volume #7 level 0.03924

> volume #7 level 0.04789

> volume #7 level 0.0575

> open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3983_007_volume_map.mrc

Opened cryosparc_P9_J3983_007_volume_map.mrc as #8, grid size 480,480,480,
pixel 0.732, shown at level 0.0105, step 2, values float32  

> volume #8 level 0.0575

> volume #8 level 0.04195

> volume #7 level 0.03636

> select add #7

3 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #3.3,0.99455,-0.074938,-0.072552,27.272,0.072407,0.99669,-0.036905,-6.1312,0.075078,0.03145,0.99668,-18.795,#7,0.99455,-0.074938,-0.072552,27.272,0.072407,0.99669,-0.036905,-6.1312,0.075078,0.03145,0.99668,-18.795

> view matrix models
> #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93,#7,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93

> fitmap #7 inMap #8

Fit map cryosparc_P9_J3984_007_volume_map.mrc in map
cryosparc_P9_J3983_007_volume_map.mrc using 49963 points  
correlation = 0.9959, correlation about mean = 0.984, overlap = 500.7  
steps = 380, shift = 16.1, angle = 34.3 degrees  
  
Position of cryosparc_P9_J3984_007_volume_map.mrc (#7) relative to
cryosparc_P9_J3983_007_volume_map.mrc (#8) coordinates:  
Matrix rotation and translation  
-0.72583440 0.68279829 -0.08337219 201.41842056  
-0.29586248 -0.41930957 -0.85828018 446.74544623  
-0.62099100 -0.59830258 0.50636370 306.03816839  
Axis 0.22676305 0.46893301 -0.85362776  
Axis point 224.32984314 270.00684921 0.00000000  
Rotation angle (degrees) 145.02379031  
Shift along axis -6.07473264  
  

> fitmap #7 inMap #8

Fit map cryosparc_P9_J3984_007_volume_map.mrc in map
cryosparc_P9_J3983_007_volume_map.mrc using 49963 points  
correlation = 0.9959, correlation about mean = 0.984, overlap = 500.7  
steps = 64, shift = 0.012, angle = 0.00824 degrees  
  
Position of cryosparc_P9_J3984_007_volume_map.mrc (#7) relative to
cryosparc_P9_J3983_007_volume_map.mrc (#8) coordinates:  
Matrix rotation and translation  
-0.72583244 0.68280184 -0.08336017 201.41856784  
-0.29596038 -0.41938679 -0.85820870 446.76271306  
-0.62094664 -0.59824441 0.50648682 306.00978970  
Axis 0.22673791 0.46887682 -0.85366530  
Axis point 224.32617617 269.99245085 0.00000000  
Rotation angle (degrees) 145.02139829  
Shift along axis -6.08403693  
  

> fitmap #7 inMap #8

Fit map cryosparc_P9_J3984_007_volume_map.mrc in map
cryosparc_P9_J3983_007_volume_map.mrc using 49963 points  
correlation = 0.9959, correlation about mean = 0.984, overlap = 500.7  
steps = 44, shift = 0.0118, angle = 0.00629 degrees  
  
Position of cryosparc_P9_J3984_007_volume_map.mrc (#7) relative to
cryosparc_P9_J3983_007_volume_map.mrc (#8) coordinates:  
Matrix rotation and translation  
-0.72584163 0.68278694 -0.08340211 201.42434440  
-0.29586571 -0.41935773 -0.85825554 446.75301724  
-0.62098100 -0.59828178 0.50640054 306.02837341  
Axis 0.22676494 0.46890903 -0.85364043  
Axis point 224.32912008 270.00287478 0.00000000  
Rotation angle (degrees) 145.02471726  
Shift along axis -6.07568669  
  

> fitmap #7 inMap #8

Fit map cryosparc_P9_J3984_007_volume_map.mrc in map
cryosparc_P9_J3983_007_volume_map.mrc using 49963 points  
correlation = 0.9959, correlation about mean = 0.984, overlap = 500.7  
steps = 100, shift = 0.0117, angle = 0.00919 degrees  
  
Position of cryosparc_P9_J3984_007_volume_map.mrc (#7) relative to
cryosparc_P9_J3983_007_volume_map.mrc (#8) coordinates:  
Matrix rotation and translation  
-0.72585579 0.68276216 -0.08348176 201.44447216  
-0.29589017 -0.41949591 -0.85817958 446.76049346  
-0.62095280 -0.59821318 0.50651615 305.99878042  
Axis 0.22676890 0.46883644 -0.85367925  
Axis point 224.32788267 269.98130269 0.00000000  
Rotation angle (degrees) 145.02655337  
Shift along axis -6.08586737  
  

> volume #8 level 0.0364

> select subtract #7

1 model selected  

> view matrix models
> #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93

> volume #7 level 0.06423

> view matrix models
> #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93

> volume #7 level 0.02003

> volume #8 level 0.02571

> volume #8 level 0.04417

> open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3969_006_volume_map.mrc

Opened cryosparc_P9_J3969_006_volume_map.mrc as #9, grid size 480,480,480,
pixel 0.732, shown at level 0.0103, step 2, values float32  

> volume #9 level 0.03176

> volume #9 level 0.01519

> open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3951_008_volume_map.mrc

Opened cryosparc_P9_J3951_008_volume_map.mrc as #10, grid size 480,480,480,
pixel 0.732, shown at level 0.0114, step 2, values float32  

> volume #!8,10 hide

> volume #10 level 0.03828

> volume #10 level 0.02869

> volume #10 level 0.04979

> fitmap #1 inMap #10

Fit map J3985_class_01_00049_volume.mrc in map
cryosparc_P9_J3951_008_volume_map.mrc using 6629 points  
correlation = 0.8689, correlation about mean = 0.602, overlap = 377  
steps = 96, shift = 1.6, angle = 4.19 degrees  
  
Position of J3985_class_01_00049_volume.mrc (#1) relative to
cryosparc_P9_J3951_008_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.99743315 -0.00176327 -0.07158214 11.61334330  
0.00282388 0.99988770 0.01471808 -3.39292521  
0.07154815 -0.01488244 0.99732611 -10.23271671  
Axis -0.20242295 -0.97879565 0.03136921  
Axis point 149.23497483 0.00000000 158.72238428  
Rotation angle (degrees) 4.19295196  
Shift along axis 0.64918094  
  

> fitmap #1 inMap #10

Fit map J3985_class_01_00049_volume.mrc in map
cryosparc_P9_J3951_008_volume_map.mrc using 6629 points  
correlation = 0.8688, correlation about mean = 0.6019, overlap = 377  
steps = 40, shift = 0.0111, angle = 0.00583 degrees  
  
Position of J3985_class_01_00049_volume.mrc (#1) relative to
cryosparc_P9_J3951_008_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.99743292 -0.00175838 -0.07158540 11.60987325  
0.00281177 0.99988921 0.01461711 -3.38346500  
0.07155176 -0.01478087 0.99732736 -10.24684374  
Axis -0.20108561 -0.97907475 0.03126035  
Axis point 149.42296601 0.00000000 158.67147531  
Rotation angle (degrees) 4.19195597  
Shift along axis 0.65776684  
  

> fitmap #1 inMap #10

Fit map J3985_class_01_00049_volume.mrc in map
cryosparc_P9_J3951_008_volume_map.mrc using 6629 points  
correlation = 0.8688, correlation about mean = 0.6019, overlap = 377  
steps = 60, shift = 0.00202, angle = 0.00304 degrees  
  
Position of J3985_class_01_00049_volume.mrc (#1) relative to
cryosparc_P9_J3951_008_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.99743293 -0.00175093 -0.07158545 11.60870841  
0.00280811 0.99988844 0.01467011 -3.38985788  
0.07155178 -0.01483347 0.99732658 -10.23757914  
Axis -0.20177899 -0.97893465 0.03117985  
Axis point 149.29375605 0.00000000 158.66352892  
Rotation angle (degrees) 4.19255884  
Shift along axis 0.65684980  
  

> fitmap #1 inMap #10

Fit map J3985_class_01_00049_volume.mrc in map
cryosparc_P9_J3951_008_volume_map.mrc using 6629 points  
correlation = 0.8688, correlation about mean = 0.6019, overlap = 377  
steps = 96, shift = 0.002, angle = 0.00324 degrees  
  
Position of J3985_class_01_00049_volume.mrc (#1) relative to
cryosparc_P9_J3951_008_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.99743159 -0.00171901 -0.07160488 11.60617014  
0.00277352 0.99988913 0.01463001 -3.37850973  
0.07157180 -0.01479103 0.99732578 -10.24880751  
Axis -0.20118700 -0.97907100 0.03072081  
Axis point 149.40364660 0.00000000 158.57590880  
Rotation angle (degrees) 4.19313151  
Shift along axis 0.65793867  
  

> open
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3989_00048_volume_series/J3989_class_01_00048_volume.mrc

Opened J3989_class_01_00048_volume.mrc as #11, grid size 128,128,128, pixel
2.74, shown at level 0.0696, step 1, values float32  

> open
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3989_00048_volume_series/J3989_class_00_00048_volume.mrc

Opened J3989_class_00_00048_volume.mrc as #12, grid size 128,128,128, pixel
2.74, shown at level 0.0695, step 1, values float32  

> volume #!1,10-12 hide

> volume #12 level 0.1515

> volume #11 level 0.1326

> volume #11 level 0.1548

> volume #1 level 0.211

> volume #2 level 0.1832

> volume #!2 hide

> open
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3968_00116_volume_series/J3968_class_01_00116_volume.mrc

Opened J3968_class_01_00116_volume.mrc as #13, grid size 144,144,144, pixel
2.75, shown at level 0.0545, step 1, values float32  

> open
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3968_00116_volume_series/J3968_class_00_00116_volume.mrc

Opened J3968_class_00_00116_volume.mrc as #14, grid size 144,144,144, pixel
2.75, shown at level 0.0495, step 1, values float32  

> volume #14 level 0.115

> volume #13 level 0.1179

> select add #13

3 models selected  

> hide #!14 models

> fitmap #13 inMap #11

Fit map J3968_class_01_00116_volume.mrc in map J3989_class_01_00048_volume.mrc
using 15819 points  
correlation = 0.8706, correlation about mean = 0.722, overlap = 2919  
steps = 140, shift = 37.7, angle = 1.37 degrees  
  
Position of J3968_class_01_00116_volume.mrc (#13) relative to
J3989_class_01_00048_volume.mrc (#11) coordinates:  
Matrix rotation and translation  
0.99971437 0.01959626 0.01368115 -28.66197852  
-0.01958627 0.99980780 -0.00086396 -16.84931847  
-0.01369545 0.00059576 0.99990604 -19.58306288  
Axis 0.03052447 0.57247681 -0.81935252  
Axis point -1036.02962297 1456.12966984 0.00000000  
Rotation angle (degrees) 1.37011058  
Shift along axis 5.52469615  
  

> fitmap #13 inMap #11

Fit map J3968_class_01_00116_volume.mrc in map J3989_class_01_00048_volume.mrc
using 15819 points  
correlation = 0.8705, correlation about mean = 0.7217, overlap = 2919  
steps = 56, shift = 0.023, angle = 0.0138 degrees  
  
Position of J3968_class_01_00116_volume.mrc (#13) relative to
J3989_class_01_00048_volume.mrc (#11) coordinates:  
Matrix rotation and translation  
0.99971346 0.01976263 0.01350659 -28.68065746  
-0.01975270 0.99980452 -0.00086839 -16.82188386  
-0.01352112 0.00060135 0.99990840 -19.61515682  
Axis 0.03068551 0.56428859 -0.82500714  
Axis point -1031.91078715 1445.31671200 0.00000000  
Rotation angle (degrees) 1.37227811  
Shift along axis 5.81016679  
  

> fitmap #11 inMap #14

Fit map J3989_class_01_00048_volume.mrc in map J3968_class_00_00116_volume.mrc
using 11649 points  
correlation = 0.8966, correlation about mean = 0.7157, overlap = 2894  
steps = 124, shift = 38, angle = 1.45 degrees  
  
Position of J3989_class_01_00048_volume.mrc (#11) relative to
J3968_class_00_00116_volume.mrc (#14) coordinates:  
Matrix rotation and translation  
0.99969266 -0.02253533 -0.01033133 28.08037343  
0.02259070 0.99973088 0.00527456 16.14208619  
0.01020969 -0.00550634 0.99993272 21.38876177  
Axis -0.21247458 -0.40483111 0.88936287  
Axis point -815.69812369 1318.66977759 0.00000000  
Rotation angle (degrees) 1.45374188  
Shift along axis 6.52118636  
  

> fitmap #11 inMap #14

Fit map J3989_class_01_00048_volume.mrc in map J3968_class_00_00116_volume.mrc
using 11649 points  
correlation = 0.8967, correlation about mean = 0.7151, overlap = 2889  
steps = 80, shift = 0.042, angle = 0.00904 degrees  
  
Position of J3989_class_01_00048_volume.mrc (#11) relative to
J3968_class_00_00116_volume.mrc (#14) coordinates:  
Matrix rotation and translation  
0.99969400 -0.02251644 -0.01024267 28.07371662  
0.02257002 0.99973202 0.00514573 16.13692320  
0.01012406 -0.00537533 0.99993430 21.40764237  
Axis -0.20801043 -0.40266782 0.89139794  
Axis point -819.63745883 1320.26275326 0.00000000  
Rotation angle (degrees) 1.44915013  
Shift along axis 6.74528284  
  

> fitmap #11 inMap #14

Fit map J3989_class_01_00048_volume.mrc in map J3968_class_00_00116_volume.mrc
using 11649 points  
correlation = 0.8965, correlation about mean = 0.7152, overlap = 2893  
steps = 80, shift = 0.0478, angle = 0.0308 degrees  
  
Position of J3989_class_01_00048_volume.mrc (#11) relative to
J3968_class_00_00116_volume.mrc (#14) coordinates:  
Matrix rotation and translation  
0.99968804 -0.02285456 -0.01007459 28.12280975  
0.02291102 0.99972224 0.00552539 16.05278061  
0.00994551 -0.00575449 0.99993398 21.48943495  
Axis -0.22026445 -0.39093637 0.89367350  
Axis point -799.73209073 1306.33286302 0.00000000  
Rotation angle (degrees) 1.46723678  
Shift along axis 6.73446774  
  

> fitmap #11 inMap #14

Fit map J3989_class_01_00048_volume.mrc in map J3968_class_00_00116_volume.mrc
using 11649 points  
correlation = 0.8965, correlation about mean = 0.7151, overlap = 2893  
steps = 64, shift = 0.00592, angle = 0.0116 degrees  
  
Position of J3989_class_01_00048_volume.mrc (#11) relative to
J3968_class_00_00116_volume.mrc (#14) coordinates:  
Matrix rotation and translation  
0.99969172 -0.02267013 -0.01012540 28.09508155  
0.02272756 0.99972605 0.00559283 16.07389740  
0.00999584 -0.00582123 0.99993310 21.49281283  
Axis -0.22401656 -0.39490657 0.89099123  
Axis point -804.48634434 1314.55289352 0.00000000  
Rotation angle (degrees) 1.45982216  
Shift along axis 6.50845650  
  

> hide #!11 models

> select subtract #13

1 model selected  

> volume #14 level 0.2241

> volume #14 level 0.06262

> volume #14 level 0.2241

> volume #14 level 0.4248

> volume #14 level 0.115

> volume #14 level 0.1717

> volume #14 level 0.211

> volume #14 level 0.1237

> volume #14 level 0.06698

> volume #14 level 0.2764

> volume #14 level 0.2241

> volume #14 level 0.2197

> volume #14 level 0.2808

> view matrix models
> #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93

> volume #14 level 0.1673

> volume #14 level 0.211

> view matrix models
> #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93

> volume #14 level 0.09752

> volume #14 level 0.1804

> volume #14 level 0.307

> volume #14 level 0.08007

> volume #14 level 0.1062

> view matrix models
> #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93

> volume #14 level 0.1542

> volume #14 level 0.1979

> view matrix models
> #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93

> volume #14 level 0.1499

> volume #14 level 0.2066

> volume #14 level 0.1019

> volume #14 level 0.1542

> volume #14 level 0.2022

> view matrix models
> #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93

> volume #14 level 0.115

> volume #14 level 0.403

> volume #14 level 0.1019

> open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3967_007_volume_map.mrc

Opened cryosparc_P9_J3967_007_volume_map.mrc as #15, grid size 324,324,324,
pixel 1.22, shown at level 0.0302, step 2, values float32  

> volume #15 level 0.08332

> volume #15 level 0.101

> volume #15 level 0.08996

> volume #15 level 0.07669

> volume #15 level 0.09438

> volume #15 level 0.163

> volume #15 level 0.1696

Segmenting cryosparc_P9_J3967_007_volume_map.mrc, density threshold 0.169599  
Showing 17 region surfaces  
1009 watershed regions, grouped to 17 regions  
Showing cryosparc_P9_J3967_007_volume_map.seg - 17 regions, 17 surfaces  
Segmenting cryosparc_P9_J3967_007_volume_map.mrc, density threshold 0.169599  
Showing 17 region surfaces  
1009 watershed regions, grouped to 17 regions  
Showing cryosparc_P9_J3967_007_volume_map.seg - 17 regions, 17 surfaces  

> select #3.17

1 model selected  
Deleted 1 regions  

> select #3.3

1 model selected  

> select clear

> select #3.1

1 model selected  

> select add #3.7

2 models selected  

> select add #3.8

3 models selected  

> select add #3.12

4 models selected  

> select add #3.10

5 models selected  

> select add #3.16

6 models selected  

> select add #3.2

7 models selected  

> select add #3.3

8 models selected  

> select add #3.11

9 models selected  

> select add #3.6

10 models selected  

> select add #3.4

11 models selected  

> select add #3.5

12 models selected  

> select subtract #3.2

11 models selected  

> select add #3.9

12 models selected  

> select clear

Drag select of 1359, 48002 of 48056 triangles, 1356, 1362, 1341, 1360, 1345,
1335, 1339, 1350, 1357, 1358, 1344, 1347, 1281, 1361, 1338, 15
cryosparc_P9_J3967_007_volume_map.mrc  

> view matrix models
> #15,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.1,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.2,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.3,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.4,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.5,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.6,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.7,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.8,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.9,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.10,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.11,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.12,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.13,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.14,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.15,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.16,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796

Saving 16 regions to mrc file...  
Opened cryosparc_P9_J3967_007_volume_map_16_regions.mrc as #16, grid size
73,125,114, pixel 1.22, shown at step 1, values float32  
Wrote cryosparc_P9_J3967_007_volume_map_16_regions.mrc  

> volume resample #16 onGrid #15

Opened cryosparc_P9_J3967_007_volume_map_16_regions.mrc resampled as #17, grid
size 324,324,324, pixel 1.22, shown at step 1, values float32  

> hide #!3 models

> volume #17 level 0.09743

> save
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3967_007_volume_map_16_regions.mrc
> models #17

> volume #16 level 0.296

> volume #16 level 0.2176

> volume #16 level 0.2393

> close #16

> close #17

> volume #15 level 0.06784

> volume #15 level 0.03687

> volume #15 level 0.0966

> volume #15 level 0.08111

> volume #15 level 0.1254

> view matrix models
> #15,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.1,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.2,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.3,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.4,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.5,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.6,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.7,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.8,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.9,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.10,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.11,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.12,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.13,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.14,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.15,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.16,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69

> close session

> open
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3977_00142_volumes/J3977_class_03_00142_volume.mrc

Opened J3977_class_03_00142_volume.mrc as #1, grid size 128,128,128, pixel
3.09, shown at level 0.0569, step 1, values float32  

> open
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3977_00142_volumes/J3977_class_02_00142_volume.mrc

Opened J3977_class_02_00142_volume.mrc as #2, grid size 128,128,128, pixel
3.09, shown at level 0.0652, step 1, values float32  

> open
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3977_00142_volumes/J3977_class_01_00142_volume.mrc

Opened J3977_class_01_00142_volume.mrc as #3, grid size 128,128,128, pixel
3.09, shown at level 0.0644, step 1, values float32  

> open
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3977_00142_volumes/J3977_class_00_00142_volume.mrc

Opened J3977_class_00_00142_volume.mrc as #4, grid size 128,128,128, pixel
3.09, shown at level 0.0511, step 1, values float32  

> surface dust #1 size 30.9

> surface dust #2 size 30.9

> surface dust #3 size 30.9

> surface dust #4 size 30.9

> volume #!1-2,4 hide

> select add #4

2 models selected  

> view matrix models
> #4,0.94781,0.16804,0.27096,-68.241,-0.31283,0.32602,0.8921,34.283,0.061569,-0.93031,0.36157,273.55

> view matrix models
> #4,0.95967,0.13122,0.24861,-59.846,-0.27903,0.33713,0.89916,24.083,0.034174,-0.93227,0.36015,279.75

> view matrix models
> #4,0.81403,-0.58022,0.026318,142.13,0.23948,0.37658,0.89489,-88.181,-0.52915,-0.72217,0.4455,340.15

> volume #3 level 0.08997

> volume #3 level 0.1412

> volume #4 level 0.1357

> view matrix models
> #4,-0.98182,-0.15393,0.11102,400.77,-0.16014,0.98586,-0.049341,48.503,-0.10186,-0.066224,-0.99259,395.11

> view matrix models
> #4,-0.88503,0.34552,0.312,251.01,0.33497,0.93805,-0.088657,-33.002,-0.3233,0.026046,-0.94594,412.92

> volume #4 level 0.3894

> volume #4 z flip

Expected a keyword  

> volume #4 zflip

Expected a keyword  

> volume #4 flipNormals

Missing "flipNormals" keyword's argument  

> volume flip #4

Opened J3977_class_00_00142_volume.mrc z flip as #5, grid size 128,128,128,
pixel 3.09, shown at step 1, values float32  

> select #5

2 models selected  

> view matrix models
> #5,-0.85933,0.30635,0.40953,234.55,-0.2375,0.47014,-0.85004,313.88,-0.45294,-0.82772,-0.33125,480.43

> fitmap #5 inMap #3

Fit map J3977_class_00_00142_volume.mrc z flip in map
J3977_class_01_00142_volume.mrc using 4563 points  
correlation = 0.9699, correlation about mean = 0.7826, overlap = 2457  
steps = 132, shift = 31.6, angle = 38.4 degrees  
  
Position of J3977_class_00_00142_volume.mrc z flip (#5) relative to
J3977_class_01_00142_volume.mrc (#3) coordinates:  
Matrix rotation and translation  
-0.99116610 0.00155516 -0.13261718 420.28508914  
0.12896783 0.24454249 -0.96102354 304.65893499  
0.03093599 -0.96963731 -0.24258280 429.65932782  
Axis -0.04151142 -0.78819365 0.61402571  
Axis point 188.06887356 0.00000000 347.37550767  
Rotation angle (degrees) 174.04473730  
Shift along axis 6.24500964  
  

> fitmap #5 inMap #3

Fit map J3977_class_00_00142_volume.mrc z flip in map
J3977_class_01_00142_volume.mrc using 4563 points  
correlation = 0.9699, correlation about mean = 0.7826, overlap = 2457  
steps = 48, shift = 0.0213, angle = 0.0281 degrees  
  
Position of J3977_class_00_00142_volume.mrc z flip (#5) relative to
J3977_class_01_00142_volume.mrc (#3) coordinates:  
Matrix rotation and translation  
-0.99117083 0.00165958 -0.13258052 420.24478315  
0.12894289 0.24500496 -0.96090909 304.53529817  
0.03088818 -0.96952039 -0.24305576 429.72894017  
Axis -0.04152874 -0.78834163 0.61383453  
Axis point 188.06053369 0.00000000 347.28922017  
Rotation angle (degrees) 174.04894559  
Shift along axis 6.25237502  
  

> volume #3 level 0.6852

> volume #5 level 0.188

> volume #3 level 0.1028

> volume #3 level 0.138

> volume #5 level 0.1598

> volume #5 level 0.1679

> volume #3 level 0.07077

> volume #3 level 0.1988

> volume #5 level 0.2806

> volume #1 level 0.2265

> fitmap #5 inMap #1

Fit map J3977_class_00_00142_volume.mrc z flip in map
J3977_class_03_00142_volume.mrc using 6115 points  
correlation = 0.9725, correlation about mean = 0.8601, overlap = 2909  
steps = 84, shift = 2.02, angle = 4.3 degrees  
  
Position of J3977_class_00_00142_volume.mrc z flip (#5) relative to
J3977_class_03_00142_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.99754203 0.02498920 -0.06546303 405.36740821  
0.06977180 0.26807185 -0.96086906 311.85792420  
-0.00646256 -0.96307476 -0.26915648 438.89272991  
Axis -0.02976493 -0.79618479 0.60432096  
Axis point 191.78070263 0.00000000 342.51916349  
Rotation angle (degrees) 177.87659093  
Shift along axis 4.86980674  
  

> fitmap #5 inMap #1

Fit map J3977_class_00_00142_volume.mrc z flip in map
J3977_class_03_00142_volume.mrc using 6115 points  
correlation = 0.9725, correlation about mean = 0.8601, overlap = 2909  
steps = 44, shift = 0.0143, angle = 0.0162 degrees  
  
Position of J3977_class_00_00142_volume.mrc z flip (#5) relative to
J3977_class_03_00142_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.99754942 0.02519611 -0.06527087 405.29719322  
0.06964248 0.26808225 -0.96087554 311.87541512  
-0.00671237 -0.96306647 -0.26918001 438.93275976  
Axis -0.02978898 -0.79618924 0.60431392  
Axis point 191.77820368 0.00000000 342.50753611  
Rotation angle (degrees) 177.89251633  
Shift along axis 4.86793646  
  

> volume #1 level 0.3043

> volume #1 level 0.2513

> volume sel hide

> volume #1 level 0.1453

> volume #4 level 0.1961

> close #4

> volume #5 level 0.2122

> volume #1 level 0.2053

> fitmap #5 inMap #1

Fit map J3977_class_00_00142_volume.mrc z flip in map
J3977_class_03_00142_volume.mrc using 7583 points  
correlation = 0.9685, correlation about mean = 0.8754, overlap = 2994  
steps = 48, shift = 0.038, angle = 0.0347 degrees  
  
Position of J3977_class_00_00142_volume.mrc z flip (#5) relative to
J3977_class_03_00142_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.99750974 0.02523858 -0.06585823 405.37295159  
0.07022047 0.26819842 -0.96080105 311.75529366  
-0.00658618 -0.96303302 -0.26930280 438.93804803  
Axis -0.02998281 -0.79622383 0.60425876  
Axis point 191.71948602 0.00000000 342.50624022  
Rotation angle (degrees) 177.86691692  
Shift along axis 4.85094606  
  

> fitmap #5 inMap #1

Fit map J3977_class_00_00142_volume.mrc z flip in map
J3977_class_03_00142_volume.mrc using 7583 points  
correlation = 0.9684, correlation about mean = 0.8752, overlap = 2994  
steps = 44, shift = 0.0584, angle = 0.026 degrees  
  
Position of J3977_class_00_00142_volume.mrc z flip (#5) relative to
J3977_class_03_00142_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.99752439 0.02490787 -0.06576214 405.45522347  
0.07003701 0.26791788 -0.96089271 311.91208460  
-0.00631494 -0.96311971 -0.26899910 438.84730228  
Axis -0.02982470 -0.79613522 0.60438332  
Axis point 191.77259653 0.00000000 342.57395662  
Rotation angle (degrees) 177.86037271  
Shift along axis 4.81521528  
  

> select subtract #5

Nothing selected  

> show #!5 models

> volume #5 level 0.2525

> hide #!5 models

> show #!1 models

> volume #1 level 0.2795

> volume #1 level 0.276

> volume #1 level 0.08519

> volume #1 level 0.1665

> volume #2 level 0.1703

> volume #2 level 0.1327

> volume #2 level 0.1928

> volume #1 level 0.223

> fitmap #1 inMap #2

Fit map J3977_class_03_00142_volume.mrc in map J3977_class_02_00142_volume.mrc
using 7452 points  
correlation = 0.9571, correlation about mean = 0.8286, overlap = 2948  
steps = 84, shift = 1.2, angle = 2.65 degrees  
  
Position of J3977_class_03_00142_volume.mrc (#1) relative to
J3977_class_02_00142_volume.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99892948 -0.04344038 -0.01590040 11.73510950  
0.04345212 0.99905543 0.00039400 -9.71668965  
0.01586826 -0.00108448 0.99987350 -3.49169470  
Axis -0.01597843 -0.34333482 0.93907715  
Axis point 230.39658326 264.41720009 0.00000000  
Rotation angle (degrees) 2.65172634  
Shift along axis -0.13040143  
  

> hide #!1 models

> volume #2 level 0.08769

> volume #2 level 0.0539

> volume #2 level 0.03889

> volume #3 level 0.03877

> volume #3 level 0.08037

> volume #2 level 0.0539

> volume #2 level 0.06517

> volume #2 level 0.07267

> volume #2 level 0.07643

> volume #2 level 0.08018

> volume #!2 hide

> volume #5 level 0.06724

> volume #5 level 0.1156

> volume #5 level 0.5102

> volume #5 level 0.3088

> volume #5 level 0.2364

> volume #5 level 0.2202

> volume #5 level 0.2162

> volume #5 level 0.2122

> volume #5 level 0.2082

> volume #5 level 0.2041

> volume #5 level 0.2001

> volume #5 level 0.1961

> volume #5 level 0.1921

> volume #5 level 0.188

> volume #5 level 0.184

> volume #5 level 0.18

> volume #5 level 0.176

> volume #5 level 0.1719

> volume #5 level 0.1679

> volume #5 level 0.1639

> volume #5 level 0.1598

> volume #5 level 0.1558

> volume #5 level 0.1518

> volume #5 level 0.1478

> volume #5 level 0.1437

> volume #5 level 0.1397

> open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3954_006_volume_map.mrc

Opened cryosparc_P9_J3954_006_volume_map.mrc as #4, grid size 324,324,324,
pixel 1.22, shown at level 0.0183, step 2, values float32  

> volume #!4-5 hide

> volume #4 level 0.06737

> volume #4 level 0.08168

> volume #4 level 0.03262

> volume #4 level 0.0551

> volume #4 level 0.0735

> ui tool show Segmentations

> ui view fourup

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen  
self._update_position_label_text()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'  
  
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen  
self._update_position_label_text()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'  
  
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen  
self._update_position_label_text()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'  
  
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> close session

> open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3954_006_volume_map.mrc

Opened cryosparc_P9_J3954_006_volume_map.mrc as #1, grid size 324,324,324,
pixel 1.22, shown at level 0.0183, step 2, values float32  

> volume #1 level 0.03022

> ui tool show "Segment Map"

> volume #1 level 0.06089

Segmenting cryosparc_P9_J3954_006_volume_map.mrc, density threshold 0.060885  
Showing 17 region surfaces  
1782 watershed regions, grouped to 17 regions  
Showing cryosparc_P9_J3954_006_volume_map.seg - 17 regions, 17 surfaces  

> select #2.4

1 model selected  
Saving 1 regions to mrc file...  
Opened cryosparc_P9_J3954_006_volume_map_region_2128.mrc as #3, grid size
42,45,72, pixel 1.22, shown at step 1, values float32  
Wrote cryosparc_P9_J3954_006_volume_map_region_2128.mrc  

> volume resample #3 onGrid #1

Opened cryosparc_P9_J3954_006_volume_map_region_2128.mrc resampled as #4, grid
size 324,324,324, pixel 1.22, shown at step 1, values float32  

> save
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3954_006_volume_map_region_2128.mrc
> models #4

> volume #1 level 0.07315

> close session

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V2_holo-
> coot-2.pdb

Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V2_holo-
coot-2.pdb  
---  
warnings | Duplicate atom serial number found: 8964  
Duplicate atom serial number found: 8965  
Duplicate atom serial number found: 8966  
Duplicate atom serial number found: 8967  
Duplicate atom serial number found: 8968  
26 messages similar to the above omitted  
  
Chain information for V2_holo-coot-2.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V3_holo-
> coot-2.pdb

Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V3_holo-
coot-2.pdb  
---  
warnings | Duplicate atom serial number found: 8964  
Duplicate atom serial number found: 8965  
Duplicate atom serial number found: 8966  
Duplicate atom serial number found: 8967  
Duplicate atom serial number found: 8968  
26 messages similar to the above omitted  
  
Chain information for V3_holo-coot-2.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V4_holo-
> coot-3.pdb

Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V4_holo-
coot-3.pdb  
---  
warnings | Duplicate atom serial number found: 8965  
Duplicate atom serial number found: 8966  
Duplicate atom serial number found: 8967  
Duplicate atom serial number found: 8968  
Duplicate atom serial number found: 8969  
30 messages similar to the above omitted  
  
Chain information for V4_holo-coot-3.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V5_holo-
> coot-1.pdb

Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V5_holo-
coot-1.pdb  
---  
warnings | Duplicate atom serial number found: 8965  
Duplicate atom serial number found: 8966  
Duplicate atom serial number found: 8967  
Duplicate atom serial number found: 8968  
Duplicate atom serial number found: 8969  
17 messages similar to the above omitted  
  
Chain information for V5_holo-coot-1.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V6_holo-
> coot-1.pdb

Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V6_holo-
coot-1.pdb  
---  
warnings | Duplicate atom serial number found: 8965  
Duplicate atom serial number found: 8966  
Duplicate atom serial number found: 8967  
Duplicate atom serial number found: 8968  
Duplicate atom serial number found: 8969  
20 messages similar to the above omitted  
  
Chain information for V6_holo-coot-1.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V7_holo-
> coot-2.pdb

Chain information for V7_holo-coot-2.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V9_holo-
> coot-0.pdb

Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V9_holo-
coot-0.pdb  
---  
warnings | Duplicate atom serial number found: 8965  
Duplicate atom serial number found: 8966  
Duplicate atom serial number found: 8967  
Duplicate atom serial number found: 8968  
Duplicate atom serial number found: 8969  
24 messages similar to the above omitted  
  
Chain information for V9_holo-coot-0.pdb #7  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V10_holo-
> coot-1.pdb

Chain information for V10_holo-coot-1.pdb #8  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V11_holo-
> coot-1.pdb

Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V11_holo-
coot-1.pdb  
---  
warnings | Duplicate atom serial number found: 8965  
Duplicate atom serial number found: 8966  
Duplicate atom serial number found: 8967  
Duplicate atom serial number found: 8968  
Duplicate atom serial number found: 8969  
29 messages similar to the above omitted  
  
Chain information for V11_holo-coot-1.pdb #9  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V12_holo-
> coot-3.pdb

Chain information for V12_holo-coot-3.pdb #10  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V14_holo-
> coot-1.pdb

Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V14_holo-
coot-1.pdb  
---  
warnings | Duplicate atom serial number found: 8964  
Duplicate atom serial number found: 8965  
Duplicate atom serial number found: 8966  
Duplicate atom serial number found: 8967  
Duplicate atom serial number found: 8968  
28 messages similar to the above omitted  
  
Chain information for V14_holo-coot-1.pdb #11  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V15_holo-
> coot-1.pdb

Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V15_holo-
coot-1.pdb  
---  
warnings | Duplicate atom serial number found: 8965  
Duplicate atom serial number found: 8966  
Duplicate atom serial number found: 8968  
Duplicate atom serial number found: 8969  
Duplicate atom serial number found: 8970  
20 messages similar to the above omitted  
  
Chain information for V15_holo-coot-1.pdb #12  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V17_holo-
> coot-3.pdb

Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V17_holo-
coot-3.pdb  
---  
warnings | Duplicate atom serial number found: 8965  
Duplicate atom serial number found: 8966  
Duplicate atom serial number found: 8967  
Duplicate atom serial number found: 8968  
Duplicate atom serial number found: 8969  
22 messages similar to the above omitted  
  
Chain information for V17_holo-coot-3.pdb #13  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V18_holo-
> coot-1.pdb

Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V18_holo-
coot-1.pdb  
---  
warnings | Duplicate atom serial number found: 8965  
Duplicate atom serial number found: 8966  
Duplicate atom serial number found: 8967  
Duplicate atom serial number found: 8968  
Duplicate atom serial number found: 8969  
24 messages similar to the above omitted  
  
Chain information for V18_holo-coot-1.pdb #14  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V19_holo-
> coot-6.pdb

Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V19_holo-
coot-6.pdb  
---  
warnings | Duplicate atom serial number found: 8965  
Duplicate atom serial number found: 8966  
Duplicate atom serial number found: 8967  
Duplicate atom serial number found: 8968  
Duplicate atom serial number found: 8969  
26 messages similar to the above omitted  
  
Chain information for V19_holo-coot-6.pdb #15  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V21_holo-
> coot-2.pdb

Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V21_holo-
coot-2.pdb  
---  
warnings | Duplicate atom serial number found: 8964  
Duplicate atom serial number found: 8965  
Duplicate atom serial number found: 8966  
Duplicate atom serial number found: 8967  
Duplicate atom serial number found: 8968  
23 messages similar to the above omitted  
  
Chain information for V21_holo-coot-2.pdb #16  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V23_holo-
> coot-2.pdb

Chain information for V23_holo-coot-2.pdb #17  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V25_holo-
> coot-2.pdb

Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V25_holo-
coot-2.pdb  
---  
warnings | Duplicate atom serial number found: 8964  
Duplicate atom serial number found: 8965  
Duplicate atom serial number found: 8966  
Duplicate atom serial number found: 8967  
Duplicate atom serial number found: 8968  
30 messages similar to the above omitted  
  
Chain information for V25_holo-coot-2.pdb #18  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Computing secondary structure  

> select #1/A:59, 60, 78, 79,49, 51, 394, 395,49, 394, 395,272, 273, 274,
> 275,113, 114, 136,277, 278, 329, 330, 331,274, 275, 276, 277, 301,256, 257,
> 258,100, 101, 102, 103, 104,100, 101, 102, 103,285, 298, 299,291, 292, 293,
> 294,299, 300, 301, 302,49, 50, 51, 388, 389, 390,59, 60, 78, 79,80, 81

983 atoms, 1091 bonds, 45 residues, 1 model selected  

> hide #2-18 target m

> select #1/A:59, 60, 78, 79,49, 51, 394, 395,49, 394, 395,272, 273, 274,
> 275,113, 114, 136,277, 278, 329, 330, 331,274, 275, 276, 277, 301,256, 257,
> 258,100, 101, 102, 103, 104,100, 101, 102, 103,285, 298, 299,291, 292, 293,
> 294,299, 300, 301, 302,49, 50, 51, 388, 389, 390,59, 60, 78, 79,80, 81

983 atoms, 1091 bonds, 45 residues, 1 model selected  

> select #8/A:100, 101, 102, 103,256, 257, 258,261, 271, 272, 273,26, 27, 28,
> 41,275, 276, 332, 333,275, 276, 333,49, 50, 51, 388, 389, 390,48, 50, 386,
> 387, 399,385, 386, 387,291, 292, 293, 294,277, 278, 329, 330, 331,275, 276,
> 333,113, 114, 136,15, 16, 17,25, 26, 274, 332,25, 26, 332,26, 274, 332,272,
> 273, 274,272, 273, 274, 275,273, 333,337, 338, 388,337, 388,382, 383,
> 384,49, 389, 390, 392, 393,49, 394, 395,49, 51, 394, 395,56, 57, 254,59, 60,
> 78, 79,61, 81, 250,80, 81

1459 atoms, 1618 bonds, 67 residues, 1 model selected  

> show #8 models

> hide #1 models

> select
> #1/A:15,21-29,39-67,69-84,96-101,105-112,249-261,272-293,295-312,327-340,386-400

3255 atoms, 3639 bonds, 151 residues, 1 model selected  

> hide #8 models

> show #1 models

> show #2-18 target m

> ui tool show Matchmaker

> matchmaker #2-18 to #1 & sel matrix Nucleic

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V3_holo-coot-2.pdb, chain A
(#2), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.380 angstroms; (across all 151 pairs:
0.413)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V4_holo-coot-3.pdb, chain A
(#3), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.322 angstroms; (across all 151 pairs:
0.322)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V5_holo-coot-1.pdb, chain A
(#4), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.445 angstroms; (across all 151 pairs:
0.445)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V6_holo-coot-1.pdb, chain A
(#5), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.365 angstroms; (across all 151 pairs:
0.365)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V7_holo-coot-2.pdb, chain A
(#6), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.323 angstroms; (across all 151 pairs:
0.323)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V9_holo-coot-0.pdb, chain A
(#7), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.325 angstroms; (across all 151 pairs:
0.325)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V10_holo-coot-1.pdb, chain A
(#8), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.364 angstroms; (across all 151 pairs:
0.364)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V11_holo-coot-1.pdb, chain A
(#9), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.374 angstroms; (across all 151 pairs:
0.374)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V12_holo-coot-3.pdb, chain A
(#10), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.367 angstroms; (across all 151 pairs:
0.367)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V14_holo-coot-1.pdb, chain A
(#11), sequence alignment score = 604  
RMSD between 149 pruned atom pairs is 0.402 angstroms; (across all 151 pairs:
0.464)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V15_holo-coot-1.pdb, chain A
(#12), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.359 angstroms; (across all 151 pairs:
0.359)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V17_holo-coot-3.pdb, chain A
(#13), sequence alignment score = 604  
RMSD between 149 pruned atom pairs is 0.351 angstroms; (across all 151 pairs:
0.441)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V18_holo-coot-1.pdb, chain A
(#14), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.367 angstroms; (across all 151 pairs:
0.367)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V19_holo-coot-6.pdb, chain A
(#15), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.488 angstroms; (across all 151 pairs:
0.488)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V21_holo-coot-2.pdb, chain A
(#16), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.445 angstroms; (across all 151 pairs:
0.445)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V23_holo-coot-2.pdb, chain A
(#17), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.368 angstroms; (across all 151 pairs:
0.368)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V25_holo-coot-2.pdb, chain A
(#18), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.430 angstroms; (across all 151 pairs:
0.430)  
  

> select

178904 atoms, 198000 bonds, 10136 residues, 18 models selected  

> hide sel target a

> select #1/C

31 atoms, 31 residues, 1 model selected  

> select #1-18/C

542 atoms, 542 residues, 18 models selected  

> show sel target ab

> style sel sphere

Changed 542 atom styles  

> hide #2-18 target m

> hide #1 models

> show #1 models

> show #2 models

> hide #1 models

> show #1 models

> hide #1 models

> show #3 models

> hide #3 models

> show #4 models

> hide #4 models

> show #5 models

> hide #5 models

> show #6 models

> hide #6 models

> show #7 models

> hide #7 models

> show #8 models

> hide #8 models

> show #9 models

> hide #9 models

> show #10 models

> hide #10 models

> show #11 models

> show #12 models

> show #13 models

> hide #13 models

> show #13 models

> hide #13 models

> show #14 models

> hide #14 models

> show #15 models

> show #16 models

> show #17 models

> hide #17 models

> show #18 models

> select #1-18/C/7

542 atoms, 542 residues, 18 models selected  

> select #1-18/C:7

18 atoms, 18 residues, 18 models selected  

> select #1-18/C:4

18 atoms, 18 residues, 18 models selected  

> select #1-18/C:24

12 atoms, 12 residues, 12 models selected  

> select clear

> hide #2 models

> hide #11 models

> hide #12 models

> hide #15 models

> hide #16 models

> hide #18 models

> show #1 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #3 models

> show #2 models

> show #4 models

> show #5 models

> hide #5 models

> show #5 models

> show #6 models

> show #7 models

> show #8 models

> show #9 models

> show #10 models

> show #11 models

> show #12 models

> show #13 models

> show #14 models

> show #15 models

> show #16 models

> show #17 models

> show #18 models

> set bgColor white

> select #1-18/A

161316 atoms, 180684 bonds, 7506 residues, 18 models selected  

> ui tool show "Color Actions"

> color sel light slate gray

> select #1-18/B

17046 atoms, 17316 bonds, 2088 residues, 18 models selected  

> ui tool show "Color Actions"

> color sel plum

> surface sel

> surface hidePatches (#!1-18 & sel)

> select #1/B

947 atoms, 962 bonds, 116 residues, 1 model selected  

> surface (#!1 & sel)

> surface hidePatches (#!1 & sel)

> surface (#!1 & sel)

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for V2_holo-coot-2.pdb_B SES surface #1.1: minimum, -9.82,
mean 5.09, maximum 22.28  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> surface hidePatches (#!1 & sel)

> select #1-18/C:1

7 atoms, 7 residues, 7 models selected  

> select #1-18/A:50,389,390

1188 atoms, 1314 bonds, 54 residues, 18 models selected  

> cartoon hide sel

> show sel target ab

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> hide sel target a

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab

> show (sel-residues & sidechain) target ab

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> hide sel target a

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> nucleotides sel atoms

> style nucleic & sel stick

Changed 1188 atom styles  

> select #1-18/A:7

360 atoms, 378 bonds, 18 residues, 18 models selected  

> select #1-18/A:50,389,390

1188 atoms, 1314 bonds, 54 residues, 18 models selected  

> color sel red

> select #6/A:392

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #15/A:393

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #3/C:68@MG

1 atom, 1 residue, 1 model selected  

> select up

35 atoms, 35 residues, 1 model selected  

> select #1-18/C:7

18 atoms, 18 residues, 18 models selected  

> ui tool show "Selection Inspector"

> size sel atomRadius 0.7

Changed 18 atom radii  

> color sel red

> select #1-18/A:50,389,390

1188 atoms, 1314 bonds, 54 residues, 18 models selected  

> ui tool show "Color Actions"

> color sel brown

> color sel coral

> color sel orange

> color sel coral

> color sel tomato

> color sel coral

> select #14/C:80@MG

1 atom, 1 residue, 1 model selected  

> select add #13/C:7@MG

2 atoms, 2 residues, 2 models selected  

> ui tool show Distances

> distance #14/C:80@MG #13/C:7@MG

Distance between V18_holo-coot-1.pdb #14/C MG 80 MG and V17_holo-coot-3.pdb
#13/C MG 7 MG: 14.313Å  

> select #10/C:80@MG

1 atom, 1 residue, 1 model selected  

> select add #12/C:7@MG

2 atoms, 2 residues, 2 models selected  

> distance #10/C:80@MG #12/C:7@MG

Distance between V12_holo-coot-3.pdb #10/C MG 80 MG and V15_holo-coot-1.pdb
#12/C MG 7 MG: 12.866Å  

> hide #!1-18 target m

> show #!1 models

> show #!2 models

> show #!3 models

> show #!4 models

> show #!5 models

> show #!6 models

> hide #!6 models

> show #!6 models

> show #!7 models

> show #!8 models

> show #!9 models

> show #!10 models

> hide #!10 models

> show #!10 models

> show #!11 models

> show #!12 models

> hide #!12 models

> show #!12 models

> show #!13 models

> show #!14 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> select #6/C:24@MG

1 atom, 1 residue, 1 model selected  

> select add #6/C:75@MG

2 atoms, 2 residues, 1 model selected  

> distance #6/C:24@MG #6/C:75@MG

Distance between V7_holo-coot-2.pdb #6/C MG 24 MG and MG 75 MG: 6.929Å  

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select add #6/C:24@MG

2 atoms, 2 residues, 2 models selected  

> distance #10/C:84@MG #6/C:24@MG

Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and V7_holo-coot-2.pdb
#6/C MG 24 MG: 3.368Å  

> select #6/C:24@MG

1 atom, 1 residue, 1 model selected  

> select add #5/C:7@MG

2 atoms, 2 residues, 2 models selected  

> distance #6/C:24@MG #5/C:7@MG

Distance between V7_holo-coot-2.pdb #6/C MG 24 MG and V6_holo-coot-1.pdb #5/C
MG 7 MG: 7.527Å  

> select #9/C:4@MG

1 atom, 1 residue, 1 model selected  

> select add #12/C:7@MG

2 atoms, 2 residues, 2 models selected  

> distance #9/C:4@MG #12/C:7@MG

Distance between V11_holo-coot-1.pdb #9/C MG 4 MG and V15_holo-coot-1.pdb
#12/C MG 7 MG: 9.036Å  

> ~distance #6/C:24@MG #6/C:75@MG

> ~distance #9/C:4@MG #12/C:7@MG

> ~distance #14/C:80@MG #13/C:7@MG

> ~distance #10/C:84@MG #6/C:24@MG

> ~distance #6/C:24@MG #5/C:7@MG

> ~distance #10/C:80@MG #12/C:7@MG

> select #1-18/A:50,389,390

1188 atoms, 1314 bonds, 54 residues, 18 models selected  

> ui tool show "Color Actions"

> color sel tomato

> color sel chocolate

> color sel fire brick

> color sel coral

> color sel goldenrod

> color (#!1-14 & sel) #ff2600ff

> color sel sienna

> color sel cyan

> color sel medium blue

> color sel cornflower blue

> select #1-18/C:7

18 atoms, 18 residues, 18 models selected  

> color (#!1-14 & sel) blue

> color sel red

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/pdb_models_YTZ/holoES-
> pretRNA-5mM-Ca/Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb

Chain information for Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb
#19  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
E | No description available  
  
Computing secondary structure  

> select up

542 atoms, 542 residues, 18 models selected  

> select up

178904 atoms, 198000 bonds, 10136 residues, 18 models selected  

> select
> #1/A:15,21-29,39-67,69-84,96-101,105-112,249-261,272-293,295-312,327-340,386-400

3255 atoms, 3639 bonds, 151 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #19 to #1 & sel matrix Nucleic

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with Ternary_pretRNA_5mM_Ca-
coot-7_real_space_refined_018.pdb, chain A (#19), sequence alignment score =
604  
RMSD between 150 pruned atom pairs is 0.728 angstroms; (across all 151 pairs:
0.766)  
  

> select #19

12016 atoms, 13315 bonds, 661 residues, 1 model selected  

> hide sel target a

> select #19/C

1889 atoms, 2107 bonds, 89 residues, 1 model selected  

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> color sel yellow

> select #19/D

30 atoms, 30 residues, 1 model selected  

> show sel target ab

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select clear

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select add #11/A:390@OP2

2 atoms, 2 residues, 2 models selected  

> distance #10/C:84@MG #11/A:390@OP2

Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and V14_holo-coot-1.pdb
#11/A A 390 OP2: 3.278Å  

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select #19/D:5@CA

1 atom, 1 residue, 1 model selected  

> select add #10/C:84@MG

2 atoms, 2 residues, 2 models selected  

> distance #19/D:5@CA #10/C:84@MG

Distance between Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb
#19/D CA 5 CA and V12_holo-coot-3.pdb #10/C MG 84 MG: 6.302Å  

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select add #19/D:30@CA

2 atoms, 2 residues, 2 models selected  

> distance #10/C:84@MG #19/D:30@CA

Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and
Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/D CA 30 CA:
7.802Å  

> hide #19 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> select #13/C:24@MG

1 atom, 1 residue, 1 model selected  

> select #9/C:24@MG

1 atom, 1 residue, 1 model selected  

> select add #10/C:84@MG

2 atoms, 2 residues, 2 models selected  

> distance #9/C:24@MG #10/C:84@MG

Distance between V11_holo-coot-1.pdb #9/C MG 24 MG and V12_holo-coot-3.pdb
#10/C MG 84 MG: 3.570Å  

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> hide #!1-14 target m

> show #!12 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> hide #!12 models

> show #!10 models

> show #19 models

> select #19/C:0

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #19/C:1

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #19/C:0

43 atoms, 46 bonds, 2 residues, 1 model selected  

> hide #19 models

> show #!1-18 target m

> select #10/C:80@MG

1 atom, 1 residue, 1 model selected  

> select clear

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> select #1-18/

Expected an objects specifier or a keyword  

> select #1-18

178904 atoms, 198000 bonds, 2 pseudobonds, 10136 residues, 19 models selected  

> select #1-18/C

542 atoms, 1 pseudobond, 542 residues, 19 models selected  

> ui tool show "Color Actions"

> color sel forest green

> select #1-18/C:7

18 atoms, 18 residues, 18 models selected  

> ui tool show "Color Actions"

> color sel dark red

> color sel maroon

> color sel dark red

> ui tool show "Selection Inspector"

> ~distance #10/C:84@MG #11/A:390@OP2

> ~distance #19/D:5@CA #10/C:84@MG

> ~distance #9/C:24@MG #10/C:84@MG

> ~distance #10/C:84@MG #19/D:30@CA

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select add #17/C:87@MG

2 atoms, 2 residues, 2 models selected  

> select #1-18/C

542 atoms, 542 residues, 18 models selected  

> ui tool show "Selection Inspector"

> size sel atomRadius 0.7

Changed 542 atom radii  

> select #13/C:22@MG

1 atom, 1 residue, 1 model selected  

> select #1-18/C:9

16 atoms, 16 residues, 16 models selected  

> color sel blue

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> select #18/C:62@MG

1 atom, 1 residue, 1 model selected  

> select add #19/A:279

21 atoms, 21 bonds, 2 residues, 2 models selected  

> select #19/C:3

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #1-18/C:12

17 atoms, 17 residues, 17 models selected  

> color sel blue

> select #18/C:62@MG

1 atom, 1 residue, 1 model selected  

> select add #19/C:3

24 atoms, 25 bonds, 2 residues, 2 models selected  

> select #19/C:3

23 atoms, 25 bonds, 1 residue, 1 model selected  

> show sel target ab

> cartoon hide sel

> select #19/C:3@C5'

1 atom, 1 residue, 1 model selected  

> select add #18/C:62@MG

2 atoms, 2 residues, 2 models selected  

> distance #19/C:3@C5' #18/C:62@MG

Distance between Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb
#19/C G 3 C5' and V25_holo-coot-2.pdb #18/C MG 62 MG: 7.071Å  

> view matrix models
> #18,0.99985,0.00571,-0.016139,1.607,-0.0060653,0.99974,-0.02205,5.6923,0.016009,0.022145,0.99963,-5.4963,#19,-0.96809,0.078949,-0.23783,410.8,0.24041,0.024802,-0.97035,327.08,-0.070709,-0.99657,-0.042991,409.72

> view matrix models
> #18,0.98188,-0.025202,-0.18781,39.726,0.0089682,0.99619,-0.086791,14.256,0.18928,0.083534,0.97836,-47.209,#19,-0.9475,0.24905,-0.20055,362.29,0.2289,0.090348,-0.96925,314.7,-0.22327,-0.96427,-0.14261,451.61

> view matrix models
> #18,0.98928,0.0045084,-0.14599,25.485,-0.014636,0.99755,-0.068373,15.45,0.14533,0.069777,0.98692,-37.485,#19,-0.95027,0.20788,-0.2319,377.78,0.25102,0.070488,-0.96541,313.97,-0.18434,-0.97561,-0.11916,442

> view matrix models
> #18,0.98454,-0.024891,-0.17338,36.644,0.017984,0.99899,-0.041293,4.3816,0.17423,0.037537,0.98399,-35.839,#19,-0.95088,0.23482,-0.20172,366.2,0.21806,0.045516,-0.97487,327.75,-0.21974,-0.97097,-0.094484,443.7

> view matrix models
> #18,0.98484,0.054997,-0.16452,19.343,-0.062648,0.99717,-0.041676,20.275,0.16176,0.051351,0.98549,-36.422,#19,-0.93307,0.22625,-0.27964,379.17,0.29591,0.040826,-0.95434,309.51,-0.2045,-0.97321,-0.10504,443.16

> matchmaker #!2-11 to #1 & sel matrix Nucleic

No 'to' model specified  

> select
> #1/A:15,21-29,39-67,69-84,96-101,105-112,249-261,272-293,295-312,327-340,386-400

3255 atoms, 3639 bonds, 151 residues, 1 model selected  

> matchmaker #!2-11 to #1 & sel matrix Nucleic

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V3_holo-coot-2.pdb, chain A
(#2), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.380 angstroms; (across all 151 pairs:
0.413)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V4_holo-coot-3.pdb, chain A
(#3), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.322 angstroms; (across all 151 pairs:
0.322)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V5_holo-coot-1.pdb, chain A
(#4), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.445 angstroms; (across all 151 pairs:
0.445)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V6_holo-coot-1.pdb, chain A
(#5), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.365 angstroms; (across all 151 pairs:
0.365)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V7_holo-coot-2.pdb, chain A
(#6), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.323 angstroms; (across all 151 pairs:
0.323)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V9_holo-coot-0.pdb, chain A
(#7), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.325 angstroms; (across all 151 pairs:
0.325)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V10_holo-coot-1.pdb, chain A
(#8), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.364 angstroms; (across all 151 pairs:
0.364)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V11_holo-coot-1.pdb, chain A
(#9), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.374 angstroms; (across all 151 pairs:
0.374)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V12_holo-coot-3.pdb, chain A
(#10), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.367 angstroms; (across all 151 pairs:
0.367)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V14_holo-coot-1.pdb, chain A
(#11), sequence alignment score = 604  
RMSD between 149 pruned atom pairs is 0.402 angstroms; (across all 151 pairs:
0.464)  
  

> matchmaker #19#!2-18 to #1 & sel matrix Nucleic

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with Ternary_pretRNA_5mM_Ca-
coot-7_real_space_refined_018.pdb, chain A (#19), sequence alignment score =
604  
RMSD between 150 pruned atom pairs is 0.728 angstroms; (across all 151 pairs:
0.766)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V3_holo-coot-2.pdb, chain A
(#2), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.380 angstroms; (across all 151 pairs:
0.413)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V4_holo-coot-3.pdb, chain A
(#3), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.322 angstroms; (across all 151 pairs:
0.322)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V5_holo-coot-1.pdb, chain A
(#4), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.445 angstroms; (across all 151 pairs:
0.445)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V6_holo-coot-1.pdb, chain A
(#5), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.365 angstroms; (across all 151 pairs:
0.365)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V7_holo-coot-2.pdb, chain A
(#6), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.323 angstroms; (across all 151 pairs:
0.323)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V9_holo-coot-0.pdb, chain A
(#7), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.325 angstroms; (across all 151 pairs:
0.325)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V10_holo-coot-1.pdb, chain A
(#8), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.364 angstroms; (across all 151 pairs:
0.364)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V11_holo-coot-1.pdb, chain A
(#9), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.374 angstroms; (across all 151 pairs:
0.374)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V12_holo-coot-3.pdb, chain A
(#10), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.367 angstroms; (across all 151 pairs:
0.367)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V14_holo-coot-1.pdb, chain A
(#11), sequence alignment score = 604  
RMSD between 149 pruned atom pairs is 0.402 angstroms; (across all 151 pairs:
0.464)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V15_holo-coot-1.pdb, chain A
(#12), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.359 angstroms; (across all 151 pairs:
0.359)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V17_holo-coot-3.pdb, chain A
(#13), sequence alignment score = 604  
RMSD between 149 pruned atom pairs is 0.351 angstroms; (across all 151 pairs:
0.441)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V18_holo-coot-1.pdb, chain A
(#14), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.367 angstroms; (across all 151 pairs:
0.367)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V19_holo-coot-6.pdb, chain A
(#15), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.488 angstroms; (across all 151 pairs:
0.488)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V21_holo-coot-2.pdb, chain A
(#16), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.445 angstroms; (across all 151 pairs:
0.445)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V23_holo-coot-2.pdb, chain A
(#17), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.368 angstroms; (across all 151 pairs:
0.368)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V25_holo-coot-2.pdb, chain A
(#18), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.430 angstroms; (across all 151 pairs:
0.430)  
  

> ui mousemode right select

> select clear

Drag select of 6 residues  

> select clear

> hide #!1-18 target m

> show #!1 models

> hide #!1 models

> show #!1 models

> show #!1-18 target m

Drag select of 17 residues  

> select clear

> select #1-18/C:10

13 atoms, 13 residues, 13 models selected  
Drag select of 6 residues  

> select #19/C:0

20 atoms, 21 bonds, 1 residue, 1 model selected  

> hide #19 models

> select #14/C:80@MG

1 atom, 1 residue, 1 model selected  

> select subtract #14/C:80@MG

Nothing selected  

> select add #5/C:24@MG

1 atom, 1 residue, 1 model selected  

> select add #14/C:80@MG

2 atoms, 2 residues, 2 models selected  

> select #7/A:278

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #14/C:80@MG

1 atom, 1 residue, 1 model selected  

> select #1-18/A:50,389,390

1188 atoms, 1314 bonds, 54 residues, 18 models selected  

> select #1-18/A:49,50,51,389,390

1998 atoms, 2232 bonds, 90 residues, 18 models selected  

> select #7/A:391

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1-18/A:49,50,51,389,390,391

2358 atoms, 2628 bonds, 108 residues, 18 models selected  

> select #1-18/A:49,50,51,52,388,389,390,391

3132 atoms, 3492 bonds, 144 residues, 18 models selected  

> show #19 models

> hide #19 models

> view sel

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select add #17/C:87@MG

2 atoms, 2 residues, 2 models selected  

> select add #1/C:4@MG

3 atoms, 3 residues, 3 models selected  

> select add #13/C:24@MG

4 atoms, 4 residues, 4 models selected  

> select add #11/A:390@OP2

5 atoms, 5 residues, 5 models selected  

> select add #12/C:7@MG

6 atoms, 6 residues, 6 models selected  

> select add #4/A:50@OP1

7 atoms, 7 residues, 7 models selected  

> view sel

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> select #7/A:390@O3'

1 atom, 1 residue, 1 model selected  

> select #7/A:390@O3'

1 atom, 1 residue, 1 model selected  

> select add #4/A:390@O2'

2 atoms, 2 residues, 2 models selected  

> select add #11/A:390@OP2

3 atoms, 3 residues, 3 models selected  

> select add #12/C:7@MG

4 atoms, 4 residues, 4 models selected  

> select add #13/C:7@MG

5 atoms, 5 residues, 5 models selected  

> select add #11/A:389@O5'

6 atoms, 6 residues, 5 models selected  

> select add #6/A:389@OP2

7 atoms, 7 residues, 6 models selected  

> select add #11/A:50@OP2

8 atoms, 8 residues, 6 models selected  

> select add #4/A:50@OP1

9 atoms, 9 residues, 6 models selected  

> select add #2/A:51

32 atoms, 25 bonds, 10 residues, 7 models selected  

> select add #17/A:49

54 atoms, 49 bonds, 11 residues, 8 models selected  

> select add #8/A:50@O2'

55 atoms, 49 bonds, 12 residues, 9 models selected  

> select add #11/A:50@O3'

56 atoms, 49 bonds, 12 residues, 9 models selected  

> select add #13/C:24@MG

57 atoms, 49 bonds, 13 residues, 9 models selected  

> select add #10/C:84@MG

58 atoms, 49 bonds, 14 residues, 10 models selected  

> select add #17/C:87@MG

59 atoms, 49 bonds, 15 residues, 10 models selected  

> select add #9/C:4@MG

60 atoms, 49 bonds, 16 residues, 11 models selected  

> view sel

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> select #13/C:7@MG

1 atom, 1 residue, 1 model selected  

> select add #17/C:82@MG

2 atoms, 2 residues, 2 models selected  

> distance #13/C:7@MG #17/C:82@MG

Distance between V17_holo-coot-3.pdb #13/C MG 7 MG and V23_holo-coot-2.pdb
#17/C MG 82 MG: 13.090Å  

> distance #13/C:7@MG #17/C:82@MG

Distance already exists; modify distance properties with 'distance style'  

> ~distance #19/C:3@C5' #18/C:62@MG

> ~distance #13/C:7@MG #17/C:82@MG

> select clear

> select #4/C:24@MG

1 atom, 1 residue, 1 model selected  

> select add #7/C:24@MG

2 atoms, 2 residues, 2 models selected  

> select add #18/C:24@MG

3 atoms, 3 residues, 3 models selected  

> select add #9/C:24@MG

4 atoms, 4 residues, 4 models selected  

> select add #3/C:24@MG

5 atoms, 5 residues, 5 models selected  

> select add #13/C:24@MG

6 atoms, 6 residues, 6 models selected  

> select add #6/C:24@MG

7 atoms, 7 residues, 7 models selected  

> select add #10/C:84@MG

8 atoms, 8 residues, 8 models selected  

> select add #17/C:87@MG

9 atoms, 9 residues, 9 models selected  

> select add #4/C:4@MG

10 atoms, 10 residues, 9 models selected  

> select add #8/C:4@MG

11 atoms, 11 residues, 10 models selected  

> select add #1/C:4@MG

12 atoms, 12 residues, 11 models selected  

> select add #9/C:4@MG

13 atoms, 13 residues, 11 models selected  

> select add #6/A:50@OP2

14 atoms, 14 residues, 11 models selected  

> select add #11/A:50@P

15 atoms, 15 residues, 12 models selected  

> select add #5/A:50@OP1

16 atoms, 16 residues, 13 models selected  

> select add #12/C:7@MG

17 atoms, 17 residues, 14 models selected  

> select add #13/C:7@MG

18 atoms, 18 residues, 14 models selected  

> select add #11/A:390@OP1

19 atoms, 19 residues, 14 models selected  

> select add #15/A:390@OP1

20 atoms, 20 residues, 15 models selected  

> select add #5/A:389@O2'

21 atoms, 21 residues, 15 models selected  

> select add #7/A:390@O2'

22 atoms, 22 residues, 15 models selected  

> select add #7/A:390@C5'

23 atoms, 22 residues, 15 models selected  

> select add #6/A:390@O5'

24 atoms, 23 residues, 15 models selected  

> select add #17/A:389@O5'

25 atoms, 24 residues, 15 models selected  

> select add #11/A:389@C4'

26 atoms, 25 residues, 15 models selected  

> select add #11/A:389@OP2

27 atoms, 25 residues, 15 models selected  

> select add #17/A:388

50 atoms, 25 bonds, 26 residues, 15 models selected  

> select add #4/A:51

73 atoms, 50 bonds, 27 residues, 15 models selected  

> select add #2/A:50@C5'

74 atoms, 50 bonds, 28 residues, 16 models selected  

> select add #4/A:50@O5'

75 atoms, 50 bonds, 29 residues, 16 models selected  

> select add #14/A:52

95 atoms, 71 bonds, 30 residues, 17 models selected  

> select add #17/A:49

117 atoms, 95 bonds, 31 residues, 17 models selected  

> view sel

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> select #3/C:68@MG

1 atom, 1 residue, 1 model selected  

> select add #13/C:7@MG

2 atoms, 2 residues, 2 models selected  

> show #19 models

> select #3/C:68@MG

1 atom, 1 residue, 1 model selected  

> select add #19/C:-1

21 atoms, 21 bonds, 2 residues, 2 models selected  
Exactly two atoms must be selected!  

> select #3/C:68@MG

1 atom, 1 residue, 1 model selected  

> hide sel target a

> hide #!18 models

> show #!18 models

> hide #19 models

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select #17/C:87@MG

1 atom, 1 residue, 1 model selected  

> show #19 models

> hide #19 models

> select clear

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select add #17/C:87@MG

2 atoms, 2 residues, 2 models selected  

> select add #13/C:7@MG

3 atoms, 3 residues, 3 models selected  

> view sel

> select add #13/C:24@MG

4 atoms, 4 residues, 3 models selected  

> select add #18/C:62@MG

5 atoms, 5 residues, 4 models selected  

> view sel

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> select #6/A:50@OP2

1 atom, 1 residue, 1 model selected  

> select add #13/C:7@MG

2 atoms, 2 residues, 2 models selected  

> select add #11/A:390@OP1

3 atoms, 3 residues, 3 models selected  

> select add #10/C:84@MG

4 atoms, 4 residues, 4 models selected  

> select add #18/C:24@MG

5 atoms, 5 residues, 5 models selected  

> select add #9/C:4@MG

6 atoms, 6 residues, 6 models selected  

> select add #4/C:4@MG

7 atoms, 7 residues, 7 models selected  

> select add #1/C:4@MG

8 atoms, 8 residues, 8 models selected  

> select add #17/C:87@MG

9 atoms, 9 residues, 9 models selected  

> select add #13/C:24@MG

10 atoms, 10 residues, 9 models selected  

> select add #6/C:24@MG

11 atoms, 11 residues, 9 models selected  

> select add #12/C:7@MG

12 atoms, 12 residues, 10 models selected  

> select add #3/C:7@MG

13 atoms, 13 residues, 11 models selected  

> select add #5/A:50@OP1

14 atoms, 14 residues, 12 models selected  

> select add #17/A:389@OP2

15 atoms, 15 residues, 12 models selected  

> select add #6/A:389@OP2

16 atoms, 16 residues, 12 models selected  

> select add #15/A:390@OP1

17 atoms, 17 residues, 13 models selected  

> select add #9/A:390@OP2

18 atoms, 18 residues, 13 models selected  

> view sel

> select #17/C:87@MG

1 atom, 1 residue, 1 model selected  

> view sel

> select #1-18/A:49,50,51,52,388,389,390,391

3132 atoms, 3492 bonds, 144 residues, 18 models selected  

> view sel

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select add #3/C:24@MG

2 atoms, 2 residues, 2 models selected  

> select add #13/C:24@MG

3 atoms, 3 residues, 3 models selected  

> select add #18/C:24@MG

4 atoms, 4 residues, 4 models selected  

> select add #9/A:390@OP2

5 atoms, 5 residues, 5 models selected  

> select add #13/C:7@MG

6 atoms, 6 residues, 5 models selected  

> select add #17/C:87@MG

7 atoms, 7 residues, 6 models selected  

> select add #1/C:4@MG

8 atoms, 8 residues, 7 models selected  

> select #1-18/A:49,50,51,52,388,389,390,391

3132 atoms, 3492 bonds, 144 residues, 18 models selected  

> select add #10/C:84@MG

3133 atoms, 3492 bonds, 145 residues, 18 models selected  

> select add #17/C:87@MG

3134 atoms, 3492 bonds, 146 residues, 18 models selected  

> select add #3/C:24@MG

3135 atoms, 3492 bonds, 147 residues, 18 models selected  

> select add #6/C:24@MG

3136 atoms, 3492 bonds, 148 residues, 18 models selected  

> select add #9/C:24@MG

3137 atoms, 3492 bonds, 149 residues, 18 models selected  

> select add #18/C:24@MG

3138 atoms, 3492 bonds, 150 residues, 18 models selected  

> select add #1/C:4@MG

3139 atoms, 3492 bonds, 151 residues, 18 models selected  

> select add #4/C:4@MG

3140 atoms, 3492 bonds, 152 residues, 18 models selected  

> select add #9/C:4@MG

3141 atoms, 3492 bonds, 153 residues, 18 models selected  

> select add #18/C:4@MG

3142 atoms, 3492 bonds, 154 residues, 18 models selected  

> select add #12/C:7@MG

3143 atoms, 3492 bonds, 155 residues, 18 models selected  

> select add #13/C:7@MG

3144 atoms, 3492 bonds, 156 residues, 18 models selected  

> select add #3/C:7@MG

3145 atoms, 3492 bonds, 157 residues, 18 models selected  

> view sel

> show #19 models

> hide #19 models

> select clear

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select clear

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select add #17/C:87@MG

2 atoms, 2 residues, 2 models selected  

> color sel magenta

> select clear

No map chosen to save  

> save
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/apo_holo_analysis/ions/ions_holo_new_core_aa_models.cxs

> show #19 models

> select #19/C:4

23 atoms, 25 bonds, 1 residue, 1 model selected  

> hide sel target a

> cartoon hide sel

> select #19/C:2

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #19/C:1

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select add #19/C:0

63 atoms, 67 bonds, 3 residues, 1 model selected  

> select #19/C:2

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #19/C:1

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select add #19/C:0

63 atoms, 67 bonds, 3 residues, 1 model selected  

> show sel target ab

> cartoon hide sel

> nucleotides sel atoms

> style nucleic & sel stick

Changed 63 atom styles  

> select #1/A:49,50,51,52,388,389,390,391

174 atoms, 194 bonds, 8 residues, 1 model selected  

> matchmaker #19 to #1 & sel matrix Nucleic

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with Ternary_pretRNA_5mM_Ca-
coot-7_real_space_refined_018.pdb, chain A (#19), sequence alignment score =
32  
RMSD between 8 pruned atom pairs is 0.305 angstroms; (across all 8 pairs:
0.305)  
  

> select #19/A

8962 atoms, 10038 bonds, 417 residues, 1 model selected  

> hide sel target a

> cartoon hide sel

> select #19/C:2

20 atoms, 21 bonds, 1 residue, 1 model selected  

> hide sel target a

> select #19/C

1889 atoms, 2107 bonds, 89 residues, 1 model selected  

> nucleotides sel tube/slab shape ellipsoid

> nucleotides sel atoms

> style nucleic & sel stick

Changed 1889 atom styles  

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> select #19/C:2-40

835 atoms, 934 bonds, 39 residues, 1 model selected  

> hide sel target a

> select #19/C

1889 atoms, 2107 bonds, 89 residues, 1 model selected  

> cartoon sel

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> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select add #17/C:87@MG

2 atoms, 2 residues, 2 models selected  

> distance #10/C:84@MG #17/C:87@MG

Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and V23_holo-coot-2.pdb
#17/C MG 87 MG: 3.390Å  

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select add #19/C:1@O3'

2 atoms, 2 residues, 2 models selected  

> distance #10/C:84@MG #19/C:1@O3'

Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and
Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/C G 1 O3': 7.687Å  

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select add #19/D:5@CA

2 atoms, 2 residues, 2 models selected  

> select #19/D:5@CA

1 atom, 1 residue, 1 model selected  

> select add #10/C:84@MG

2 atoms, 2 residues, 2 models selected  

> distance #19/D:5@CA #10/C:84@MG

Distance between Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb
#19/D CA 5 CA and V12_holo-coot-3.pdb #10/C MG 84 MG: 6.681Å  

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select add #19/D:6@CA

2 atoms, 2 residues, 2 models selected  

> distance #10/C:84@MG #19/D:6@CA

Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and
Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/D CA 6 CA: 2.783Å  

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select add #3/C:24@MG

2 atoms, 2 residues, 2 models selected  

> distance #10/C:84@MG #3/C:24@MG

Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and V4_holo-coot-3.pdb
#3/C MG 24 MG: 3.250Å  

> select #17/C:87@MG

1 atom, 1 residue, 1 model selected  

> select add #19/D:6@CA

2 atoms, 2 residues, 2 models selected  

> distance #17/C:87@MG #19/D:6@CA

Distance between V23_holo-coot-2.pdb #17/C MG 87 MG and
Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/D CA 6 CA: 5.916Å  

> select #17/C:87@MG

1 atom, 1 residue, 1 model selected  

> select add #19/C:1@O3'

2 atoms, 2 residues, 2 models selected  

> distance #17/C:87@MG #19/C:1@O3'

Distance between V23_holo-coot-2.pdb #17/C MG 87 MG and
Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/C G 1 O3': 4.880Å  

> select #17/C:87@MG

1 atom, 1 residue, 1 model selected  

> select add #19/D:5@CA

2 atoms, 2 residues, 2 models selected  

> distance #17/C:87@MG #19/D:5@CA

Distance between V23_holo-coot-2.pdb #17/C MG 87 MG and
Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/D CA 5 CA: 6.174Å  

> select #17/C:87@MG

1 atom, 1 residue, 1 model selected  

> select add #19/C:1@OP1

2 atoms, 2 residues, 2 models selected  

> distance #17/C:87@MG #19/C:1@OP1

Distance between V23_holo-coot-2.pdb #17/C MG 87 MG and
Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/C G 1 OP1: 6.874Å  

> select #19/D:5@CA

1 atom, 1 residue, 1 model selected  

> select add #19/C:1@OP1

2 atoms, 2 residues, 1 model selected  

> distance #19/D:5@CA #19/C:1@OP1

Distance between Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb
#19/D CA 5 CA and /C G 1 OP1: 2.234Å  

> select #19/D:7@CA

1 atom, 1 residue, 1 model selected  

> select add #19/C:1@OP2

2 atoms, 2 residues, 1 model selected  

> distance #19/D:7@CA #19/C:1@OP2

Distance between Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb
#19/D CA 7 CA and /C G 1 OP2: 2.625Å  

> ~distance #10/C:84@MG #17/C:87@MG

> ~distance #19/D:5@CA #10/C:84@MG

> ~distance #10/C:84@MG #19/C:1@O3'

> ~distance #19/D:7@CA #19/C:1@OP2

> ~distance #17/C:87@MG #19/C:1@O3'

> ~distance #19/D:5@CA #19/C:1@OP1

> ~distance #17/C:87@MG #19/C:1@OP1

> ~distance #10/C:84@MG #19/D:6@CA

> ~distance #17/C:87@MG #19/D:5@CA

> ~distance #10/C:84@MG #3/C:24@MG

> ~distance #17/C:87@MG #19/D:6@CA

> color sel #5f5f5fff

> color sel #5f5f5ffe

> color sel #5f5f5ffd

> color sel #5f5f5ffc

> color sel #5f5f5ffb

> color sel #5f5f5ffa

> color sel #5f5f5ff9

> color sel #5f5f5ff8

> color sel #5f5f5ff7

> color sel #5f5f5ff6

> color sel #5f5f5ff5

> color sel #5f5f5ff3

> color sel #5f5f5ff2

> color sel #5f5f5ff1

> color sel #5f5f5ff0

> color sel #5f5f5fee

> color sel #5f5f5fec

> color sel #5f5f5feb

> color sel #5f5f5fea

> color sel #5f5f5fe9

> color sel #5f5f5fe8

> color sel #5f5f5fe7

> select #19/C

1889 atoms, 2107 bonds, 89 residues, 1 model selected  

> lighting simple

> lighting soft

> lighting full

> lighting soft

> lighting simple

> lighting soft

> lighting simple

> color sel #5f5f5fe7

> color sel #5f5f5fe6

> color sel #5f5f5fe3

> color sel #5f5f5fe2

> color sel #5f5f5fe1

> color sel #5f5f5fe0

> color sel #5f5f5fdf

> color sel #5f5f5fde

> color sel #5f5f5fdd

> color sel #5f5f5fdc

> color sel #5f5f5fda

> color sel #5f5f5fd8

> color sel #5f5f5fd6

> color sel #5f5f5fd4

> color sel #5f5f5fd2

> color sel #5f5f5fd1

> color sel #5f5f5fd0

> color sel #5f5f5fcf

> color sel #5f5f5fcd

> color sel #5f5f5fcc

> color sel #5f5f5fca

> color sel #5f5f5fc9

> color sel #5f5f5fc7

> color sel #5f5f5fc5

> color sel #5f5f5fc1

> color sel #5f5f5fbf

> color sel #5f5f5fbd

> color sel #5f5f5fbb

> color sel #5f5f5fba

> color sel #5f5f5fb8

> color sel #5f5f5fb5

> color sel #5f5f5fb4

> color sel #5f5f5fb1

> color sel #5f5f5fb0

> color sel #5f5f5fae

> color sel #5f5f5fad

> color sel #5f5f5fac

> color sel #5f5f5fab

> color sel #5f5f5fa9

> color sel #5f5f5fa7

> color sel #5f5f5fa3

> color sel #5f5f5f9f

> color sel #5f5f5f9b

> color sel #5f5f5f99

> color sel #5f5f5f96

> color sel #5f5f5f95

> color sel #5f5f5f94

> color sel #5f5f5f93

> color sel #5f5f5f92

> color sel #5f5f5f90

> color sel #5f5f5f8f

> color sel #5f5f5f8e

> color sel #5f5f5f8d

> color sel #5f5f5f8c

> color sel #5f5f5f8b

> color sel #5f5f5f89

> color sel #5f5f5f88

> color sel #5f5f5f87

> color sel #5f5f5f85

> color sel #5f5f5f84

> color sel #5f5f5f83

> color sel #5f5f5f84

> color sel #5f5f5f87

> color sel #5f5f5f8d

> color sel #5f5f5f95

> color sel #5f5f5f99

> color sel #5f5f5f9d

> color sel #5f5f5f9f

> color sel #5f5f5fa1

> color sel #5f5f5fa3

> color sel #5f5f5fa4

> color sel #5f5f5fa5

> color sel #5f5f5fa6

> color sel #5f5f5fa8

> color sel #5f5f5fab

> color sel #5f5f5fad

> color sel #5f5f5fae

> color sel #5f5f5faf

> color sel #5f5f5fb1

> color sel #5f5f5fb2

> color sel #5f5f5fb5

> color sel #5f5f5fb6

> color sel #5f5f5fb7

> color sel #5f5f5fb8

> color sel #5f5f5fb9

> color sel #5f5f5fbb

> color sel #5f5f5fbd

> color sel #5f5f5fc1

> color sel #5f5f5fc7

> color sel #5f5f5fcc

> color sel #5f5f5fcf

> color sel #5f5f5fd0

> color sel #5f5f5fce

> color sel #5f5f5fc2

> color sel #5f5f5fb8

> color sel #5f5f5fb2

> color sel #5f5f5fb1

> color sel #5f5f5fb0

> color sel #5f5f5fad

> color sel #5f5f5fab

> color sel #5f5f5fa9

> color sel #5f5f5fa5

> color sel #5f5f5fa3

> select #19/D:30@CA

1 atom, 1 residue, 1 model selected  

> select add #19/D:5@CA

2 atoms, 2 residues, 1 model selected  

> color sel #404040ff

> select #19/D:7@CA

1 atom, 1 residue, 1 model selected  

> select #19/D:7@CA

1 atom, 1 residue, 1 model selected  

> color sel #404040ff

> color sel #3f3f3fff

> color sel #3e3e3eff

> color sel #3d3d3dff

> color sel #3c3c3cff

> color sel #3d3d3dff

> select #19/D:6@CA

1 atom, 1 residue, 1 model selected  

> select add #19/D:1@CA

2 atoms, 2 residues, 1 model selected  

> select add #19/D:3@CA

3 atoms, 3 residues, 1 model selected  

> color sel #4f8f00ff

> color sel #005493ff

> select clear

> save
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/apo_holo_analysis/ions/ions_holo_new_core_aa_models_ternary_comp.cxs

> hide #19 models

> save ions_core_holo.png supersample 3 transparentBackground true

> lighting simple

> lighting soft

> lighting simple

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> ui tool show "Side View"

> lighting soft

> lighting simple

> lighting soft

> save ions_core_holo_2.png supersample 3 transparentBackground true

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select add #11/A:390@OP2

2 atoms, 2 residues, 2 models selected  

> distance #10/C:84@MG #11/A:390@OP2

Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and V14_holo-coot-1.pdb
#11/A A 390 OP2: 3.278Å  

> select #6/C:24@MG

1 atom, 1 residue, 1 model selected  

> select add #6/A:390@OP2

2 atoms, 2 residues, 1 model selected  

> distance #6/C:24@MG #6/A:390@OP2

Distance between V7_holo-coot-2.pdb #6/C MG 24 MG and /A A 390 OP2: 4.213Å  

> select #6/C:24@MG

1 atom, 1 residue, 1 model selected  

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select clear

> select #17/C:87@MG

1 atom, 1 residue, 1 model selected  

> select add #11/A:390@OP2

2 atoms, 2 residues, 2 models selected  

> distance #17/C:87@MG #11/A:390@OP2

Distance between V23_holo-coot-2.pdb #17/C MG 87 MG and V14_holo-coot-1.pdb
#11/A A 390 OP2: 4.350Å  

> ~distance #6/C:24@MG #6/A:390@OP2

> ~distance #10/C:84@MG #11/A:390@OP2

> ~distance #17/C:87@MG #11/A:390@OP2

> select clear

> lighting simple

> toolshed show

> select #18/C:24@MG

1 atom, 1 residue, 1 model selected  

> select add #11/A:390@OP2

2 atoms, 2 residues, 2 models selected  

> distance #18/C:24@MG #11/A:390@OP2

Distance between V25_holo-coot-2.pdb #18/C MG 24 MG and V14_holo-coot-1.pdb
#11/A A 390 OP2: 4.140Å  

> select #17/A:50@OP2

1 atom, 1 residue, 1 model selected  

> select add #9/C:4@MG

2 atoms, 2 residues, 2 models selected  

> distance #17/A:50@OP2 #9/C:4@MG

Distance between V23_holo-coot-2.pdb #17/A A 50 OP2 and V11_holo-coot-1.pdb
#9/C MG 4 MG: 5.979Å  

> select #11/A:390@OP2

1 atom, 1 residue, 1 model selected  

> select add #10/C:84@MG

2 atoms, 2 residues, 2 models selected  

> distance #11/A:390@OP2 #10/C:84@MG

Distance between V14_holo-coot-1.pdb #11/A A 390 OP2 and V12_holo-coot-3.pdb
#10/C MG 84 MG: 3.278Å  

> select #17/C:87@MG

1 atom, 1 residue, 1 model selected  

> select add #10/C:84@MG

2 atoms, 2 residues, 2 models selected  

> distance #17/C:87@MG #10/C:84@MG

Distance between V23_holo-coot-2.pdb #17/C MG 87 MG and V12_holo-coot-3.pdb
#10/C MG 84 MG: 3.390Å  

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select add #17/C:87@MG

2 atoms, 2 residues, 2 models selected  

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> color sel lime

> color sel purple

> ~distance #11/A:390@OP2 #10/C:84@MG

> ~distance #17/A:50@OP2 #9/C:4@MG

> ~distance #17/C:87@MG #10/C:84@MG

> ~distance #18/C:24@MG #11/A:390@OP2

> select clear

> select #7/C:24@MG

1 atom, 1 residue, 1 model selected  

> select add #7/A:390@C5'

2 atoms, 2 residues, 1 model selected  

> distance #7/C:24@MG #7/A:390@C5'

Distance between V9_holo-coot-0.pdb #7/C MG 24 MG and /A A 390 C5': 5.156Å  

> select clear

> select #7/C:24@MG

1 atom, 1 residue, 1 model selected  

> select add #11/A:390@OP2

2 atoms, 2 residues, 2 models selected  

> distance #7/C:24@MG #11/A:390@OP2

Distance between V9_holo-coot-0.pdb #7/C MG 24 MG and V14_holo-coot-1.pdb
#11/A A 390 OP2: 4.308Å  

> select #3/C:24@MG

1 atom, 1 residue, 1 model selected  

> select add #11/A:390@OP2

2 atoms, 2 residues, 2 models selected  

> distance #3/C:24@MG #11/A:390@OP2

Distance between V4_holo-coot-3.pdb #3/C MG 24 MG and V14_holo-coot-1.pdb
#11/A A 390 OP2: 4.180Å  

> select #13/C:24@MG

1 atom, 1 residue, 1 model selected  

> select #11/A:390@OP2

1 atom, 1 residue, 1 model selected  

> select add #13/C:24@MG

2 atoms, 2 residues, 2 models selected  

> distance #11/A:390@OP2 #13/C:24@MG

Distance between V14_holo-coot-1.pdb #11/A A 390 OP2 and V17_holo-coot-3.pdb
#13/C MG 24 MG: 4.168Å  

> select #4/C:24@MG

1 atom, 1 residue, 1 model selected  

> select add #11/A:390@OP2

2 atoms, 2 residues, 2 models selected  

> distance #4/C:24@MG #11/A:390@OP2

Distance between V5_holo-coot-1.pdb #4/C MG 24 MG and V14_holo-coot-1.pdb
#11/A A 390 OP2: 4.683Å  

> ~distance #7/C:24@MG #7/A:390@C5'

> ~distance #4/C:24@MG #11/A:390@OP2

> ~distance #3/C:24@MG #11/A:390@OP2

> ~distance #7/C:24@MG #11/A:390@OP2

> ~distance #11/A:390@OP2 #13/C:24@MG

> select clear

> save ions_core_holo_2.png supersample 3 transparentBackground true

> save
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/apo_holo_analysis/ions/ions_holo_new_core_aa_models.cxs

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V1_Mg-
> coot-1.pdb

Chain information for V1_Mg-coot-1.pdb #20  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V2_Mg-
> coot-1.pdb

Chain information for V2_Mg-coot-1.pdb #21  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V3_Mg-
> coot-2.pdb

Chain information for V3_Mg-coot-2.pdb #22  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V4_Mg-
> coot-2.pdb

Chain information for V4_Mg-coot-2.pdb #23  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V5_Mg-
> coot-1.pdb

Chain information for V5_Mg-coot-1.pdb #24  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V6_Mg-
> coot-1.pdb

Chain information for V6_Mg-coot-1.pdb #25  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V7_Mg-
> coot-2.pdb

Chain information for V7_Mg-coot-2.pdb #26  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V8_Mg-
> coot-2.pdb

Chain information for V8_Mg-coot-2.pdb #27  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V9_Mg-
> coot-3.pdb

Chain information for V9_Mg-coot-3.pdb #28  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V10_Mg-
> coot-3.pdb

Chain information for V10_Mg-coot-3.pdb #29  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V11_Mg-
> coot-2.pdb

Chain information for V11_Mg-coot-2.pdb #30  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V12_real_space_refined_011-coot-0.pdb

Chain information for V12_real_space_refined_011-coot-0.pdb #31  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V13_Mg-
> coot-2.pdb

Chain information for V13_Mg-coot-2.pdb #32  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V13_Mg-
> coot-3_6.pdb

Chain information for V13_Mg-coot-3_6.pdb #33  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V14_Mg-
> coot-1.pdb

Chain information for V14_Mg-coot-1.pdb #34  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V15_Mg-
> coot-2.pdb

Chain information for V15_Mg-coot-2.pdb #35  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V16_Mg-
> coot-1.pdb

Chain information for V16_Mg-coot-1.pdb #36  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V17_Mg-
> coot-2.pdb

Chain information for V17_Mg-coot-2.pdb #37  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V18_Mg-
> coot-1.pdb

Chain information for V18_Mg-coot-1.pdb #38  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V19_Mg-
> coot-3.pdb

Chain information for V19_Mg-coot-3.pdb #39  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V20_Mg-
> coot-2.pdb

Chain information for V20_Mg-coot-2.pdb #40  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V21_Mg_real_space_refined_002-coot-1.pdb

Chain information for V21_Mg_real_space_refined_002-coot-1.pdb #41  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V22_Mg_6sig.pdb

Chain information for V22_Mg_6sig.pdb #42  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V22_Mg_real_space_refined_002-coot-1.pdb

Chain information for V22_Mg_real_space_refined_002-coot-1.pdb #43  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V23_Mg_6sig.pdb

Chain information for V23_Mg_6sig.pdb #44  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V23_Mg-
> coot-1.pdb

Chain information for V23_Mg-coot-1.pdb #45  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V24_6sig.pdb

Chain information for V24_6sig.pdb #46  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V24_Mg-
> coot-6.pdb

Chain information for V24_Mg-coot-6.pdb #47  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V25_Mg-
> coot-1.pdb

Chain information for V25_Mg-coot-1.pdb #48  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V26_Mg-
> coot-1.pdb

Chain information for V26_Mg-coot-1.pdb #49  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V27_Mg-
> coot-2.pdb

Chain information for V27_Mg-coot-2.pdb #50  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V28_Mg-
> coot-1.pdb

Chain information for V28_Mg-coot-1.pdb #51  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V29_Mg-
> coot-2.pdb

Chain information for V29_Mg-coot-2.pdb #52  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V30_Mg-
> coot-3.pdb

Chain information for V30_Mg-coot-3.pdb #53  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V31_Mg-
> coot-3.pdb

Chain information for V31_Mg-coot-3.pdb #54  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V32_Mg-
> coot-2.pdb

Chain information for V32_Mg-coot-2.pdb #55  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V33_Mg-
> coot-2.pdb

Chain information for V33_Mg-coot-2.pdb #56  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V34_Mg-
> coot-3.pdb

Chain information for V34_Mg-coot-3.pdb #57  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V35_Mg-
> coot-2.pdb

Chain information for V35_Mg-coot-2.pdb #58  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V36_Mg-
> coot-1.pdb

Chain information for V36_Mg-coot-1.pdb #59  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V37_Mg-
> coot-1.pdb

Chain information for V37_Mg-coot-1.pdb #60  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V38_Mg-
> coot-1.pdb

Chain information for V38_Mg-coot-1.pdb #61  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V39_Mg_real_space_refined_002-coot-0.pdb

Chain information for V39_Mg_real_space_refined_002-coot-0.pdb #62  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V40_Mg_real_space_refined_003-coot-0_aligned.pdb

Chain information for V40_Mg_real_space_refined_003-coot-0_aligned.pdb #63  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V40_Mg_real_space_refined_003-coot-0.pdb

Chain information for V40_Mg_real_space_refined_003-coot-0.pdb #64  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V41_Mg_real_space_refined_003-coot-0.pdb

Chain information for V41_Mg_real_space_refined_003-coot-0.pdb #65  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V42_Mg_real_space_refined_003-coot-0.pdb

Chain information for V42_Mg_real_space_refined_003-coot-0.pdb #66  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V43_Mg_real_space_refined_001-coot-0.pdb

Chain information for V43_Mg_real_space_refined_001-coot-0.pdb #67  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V44_Mg_real_space_refined_003-coot-0.pdb

Chain information for V44_Mg_real_space_refined_003-coot-0.pdb #68  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V45_Mg-
> coot-3.pdb

Chain information for V45_Mg-coot-3.pdb #69  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V46_Mg-
> coot-2.pdb

Chain information for V46_Mg-coot-2.pdb #70  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V47_Mg-
> coot-4.pdb

Chain information for V47_Mg-coot-4.pdb #71  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V48_Mg-
> coot-1.pdb

Chain information for V48_Mg-coot-1.pdb #72  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V49_Mg-
> coot-2.pdb

Chain information for V49_Mg-coot-2.pdb #73  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V1_holo_set_noprot-
> coot-2.pdb

Chain information for V1_holo_set_noprot-coot-2.pdb #74  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V8_holo_no_prot_a-
> coot-4.pdb

Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V8_holo_no_prot_a-
coot-4.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ASN B 10 GLN B 19 1 10  
Start residue of secondary structure not found: HELIX 2 2 ALA B 54 GLU B 70 1
17  
Start residue of secondary structure not found: HELIX 3 3 GLN B 87 ALA B 89 1
3  
Start residue of secondary structure not found: HELIX 4 4 TYR B 94 LYS B 107 1
14  
Start residue of secondary structure not found: SHEET 1 1 1 PHE B 28 ASP B 34
0  
2 messages similar to the above omitted  
  
Chain information for V8_holo_no_prot_a-coot-4.pdb #75  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V13_holo_set_noapo-
> coot-3.pdb

Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V13_holo_set_noapo-
coot-3.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ASN B 10 GLN B 19 1 10  
Start residue of secondary structure not found: HELIX 2 2 ALA B 54 GLU B 70 1
17  
Start residue of secondary structure not found: HELIX 3 3 GLN B 87 ALA B 89 1
3  
Start residue of secondary structure not found: HELIX 4 4 TYR B 94 LYS B 107 1
14  
Start residue of secondary structure not found: SHEET 1 1 1 PHE B 28 ASP B 34
0  
2 messages similar to the above omitted  
  
Chain information for V13_holo_set_noapo-coot-3.pdb #76  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V20_holo_no_prot-
> coot-1.pdb

Chain information for V20_holo_no_prot-coot-1.pdb #77  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V22_holo_no_prot-
> coot-1.pdb

Chain information for V22_holo_no_prot-coot-1.pdb #78  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V24_holo_no_prot-
> coot-3.pdb

Chain information for V24_holo_no_prot-coot-3.pdb #79  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> select
> #1/A:15,21-29,39-67,69-84,96-101,105-112,249-261,272-293,295-312,327-340,386-400

3255 atoms, 3639 bonds, 151 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #20-49,51-79#!50 to #1 & sel matrix Nucleic

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V1_Mg-coot-1.pdb, chain A
(#20), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.460 angstroms; (across all 151 pairs:
0.510)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V2_Mg-coot-1.pdb, chain A
(#21), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.443 angstroms; (across all 151 pairs:
0.490)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V3_Mg-coot-2.pdb, chain A
(#22), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.478 angstroms; (across all 151 pairs:
0.530)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V4_Mg-coot-2.pdb, chain A
(#23), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.470 angstroms; (across all 151 pairs:
0.515)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V5_Mg-coot-1.pdb, chain A
(#24), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.472 angstroms; (across all 151 pairs:
0.521)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V6_Mg-coot-1.pdb, chain A
(#25), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.469 angstroms; (across all 151 pairs:
0.519)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V7_Mg-coot-2.pdb, chain A
(#26), sequence alignment score = 604  
RMSD between 148 pruned atom pairs is 0.517 angstroms; (across all 151 pairs:
0.622)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V8_Mg-coot-2.pdb, chain A
(#27), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.465 angstroms; (across all 151 pairs:
0.504)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V9_Mg-coot-3.pdb, chain A
(#28), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.490 angstroms; (across all 151 pairs:
0.523)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V10_Mg-coot-3.pdb, chain A
(#29), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.491 angstroms; (across all 151 pairs:
0.532)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V11_Mg-coot-2.pdb, chain A
(#30), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.480 angstroms; (across all 151 pairs:
0.536)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
V12_real_space_refined_011-coot-0.pdb, chain A (#31), sequence alignment score
= 604  
RMSD between 150 pruned atom pairs is 0.523 angstroms; (across all 151 pairs:
0.559)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V13_Mg-coot-2.pdb, chain A
(#32), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.504 angstroms; (across all 151 pairs:
0.540)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V13_Mg-coot-3_6.pdb, chain A
(#33), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.504 angstroms; (across all 151 pairs:
0.540)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V14_Mg-coot-1.pdb, chain A
(#34), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.477 angstroms; (across all 151 pairs:
0.534)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V15_Mg-coot-2.pdb, chain A
(#35), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.461 angstroms; (across all 151 pairs:
0.518)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V16_Mg-coot-1.pdb, chain A
(#36), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.452 angstroms; (across all 151 pairs:
0.506)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V17_Mg-coot-2.pdb, chain A
(#37), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.439 angstroms; (across all 151 pairs:
0.502)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V18_Mg-coot-1.pdb, chain A
(#38), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.461 angstroms; (across all 151 pairs:
0.498)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V19_Mg-coot-3.pdb, chain A
(#39), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.458 angstroms; (across all 151 pairs:
0.496)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V20_Mg-coot-2.pdb, chain A
(#40), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.458 angstroms; (across all 151 pairs:
0.520)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
V21_Mg_real_space_refined_002-coot-1.pdb, chain A (#41), sequence alignment
score = 604  
RMSD between 150 pruned atom pairs is 0.480 angstroms; (across all 151 pairs:
0.525)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V22_Mg_6sig.pdb, chain A
(#42), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.449 angstroms; (across all 151 pairs:
0.508)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
V22_Mg_real_space_refined_002-coot-1.pdb, chain A (#43), sequence alignment
score = 604  
RMSD between 150 pruned atom pairs is 0.449 angstroms; (across all 151 pairs:
0.508)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V23_Mg_6sig.pdb, chain A
(#44), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.495 angstroms; (across all 151 pairs:
0.534)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V23_Mg-coot-1.pdb, chain A
(#45), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.495 angstroms; (across all 151 pairs:
0.534)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V24_6sig.pdb, chain A (#46),
sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.487 angstroms; (across all 151 pairs:
0.552)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V24_Mg-coot-6.pdb, chain A
(#47), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.487 angstroms; (across all 151 pairs:
0.552)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V25_Mg-coot-1.pdb, chain A
(#48), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.465 angstroms; (across all 151 pairs:
0.518)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V26_Mg-coot-1.pdb, chain A
(#49), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.491 angstroms; (across all 151 pairs:
0.546)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V28_Mg-coot-1.pdb, chain A
(#51), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.514 angstroms; (across all 151 pairs:
0.557)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V29_Mg-coot-2.pdb, chain A
(#52), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.486 angstroms; (across all 151 pairs:
0.512)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V30_Mg-coot-3.pdb, chain A
(#53), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.427 angstroms; (across all 151 pairs:
0.470)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V31_Mg-coot-3.pdb, chain A
(#54), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.462 angstroms; (across all 151 pairs:
0.524)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V32_Mg-coot-2.pdb, chain A
(#55), sequence alignment score = 604  
RMSD between 149 pruned atom pairs is 0.454 angstroms; (across all 151 pairs:
0.624)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V33_Mg-coot-2.pdb, chain A
(#56), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.472 angstroms; (across all 151 pairs:
0.515)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V34_Mg-coot-3.pdb, chain A
(#57), sequence alignment score = 604  
RMSD between 149 pruned atom pairs is 0.539 angstroms; (across all 151 pairs:
0.609)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V35_Mg-coot-2.pdb, chain A
(#58), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.538 angstroms; (across all 151 pairs:
0.577)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V36_Mg-coot-1.pdb, chain A
(#59), sequence alignment score = 604  
RMSD between 149 pruned atom pairs is 0.505 angstroms; (across all 151 pairs:
0.589)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V37_Mg-coot-1.pdb, chain A
(#60), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.476 angstroms; (across all 151 pairs:
0.520)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V38_Mg-coot-1.pdb, chain A
(#61), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.462 angstroms; (across all 151 pairs:
0.509)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
V39_Mg_real_space_refined_002-coot-0.pdb, chain A (#62), sequence alignment
score = 604  
RMSD between 150 pruned atom pairs is 0.495 angstroms; (across all 151 pairs:
0.539)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
V40_Mg_real_space_refined_003-coot-0_aligned.pdb, chain A (#63), sequence
alignment score = 604  
RMSD between 149 pruned atom pairs is 0.522 angstroms; (across all 151 pairs:
0.591)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
V40_Mg_real_space_refined_003-coot-0.pdb, chain A (#64), sequence alignment
score = 604  
RMSD between 149 pruned atom pairs is 0.526 angstroms; (across all 151 pairs:
0.595)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
V41_Mg_real_space_refined_003-coot-0.pdb, chain A (#65), sequence alignment
score = 604  
RMSD between 150 pruned atom pairs is 0.484 angstroms; (across all 151 pairs:
0.540)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
V42_Mg_real_space_refined_003-coot-0.pdb, chain A (#66), sequence alignment
score = 604  
RMSD between 150 pruned atom pairs is 0.482 angstroms; (across all 151 pairs:
0.526)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
V43_Mg_real_space_refined_001-coot-0.pdb, chain A (#67), sequence alignment
score = 604  
RMSD between 149 pruned atom pairs is 0.513 angstroms; (across all 151 pairs:
0.602)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
V44_Mg_real_space_refined_003-coot-0.pdb, chain A (#68), sequence alignment
score = 604  
RMSD between 150 pruned atom pairs is 0.507 angstroms; (across all 151 pairs:
0.549)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V45_Mg-coot-3.pdb, chain A
(#69), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.494 angstroms; (across all 151 pairs:
0.546)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V46_Mg-coot-2.pdb, chain A
(#70), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.436 angstroms; (across all 151 pairs:
0.490)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V47_Mg-coot-4.pdb, chain A
(#71), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.564 angstroms; (across all 151 pairs:
0.596)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V48_Mg-coot-1.pdb, chain A
(#72), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.468 angstroms; (across all 151 pairs:
0.523)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V49_Mg-coot-2.pdb, chain A
(#73), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.461 angstroms; (across all 151 pairs:
0.529)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V1_holo_set_noprot-
coot-2.pdb, chain A (#74), sequence alignment score = 604  
RMSD between 149 pruned atom pairs is 0.402 angstroms; (across all 151 pairs:
0.464)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V8_holo_no_prot_a-coot-4.pdb,
chain A (#75), sequence alignment score = 604  
RMSD between 149 pruned atom pairs is 0.486 angstroms; (across all 151 pairs:
0.562)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V13_holo_set_noapo-
coot-3.pdb, chain A (#76), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.491 angstroms; (across all 151 pairs:
0.491)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V20_holo_no_prot-coot-1.pdb,
chain A (#77), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.442 angstroms; (across all 151 pairs:
0.442)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V22_holo_no_prot-coot-1.pdb,
chain A (#78), sequence alignment score = 604  
RMSD between 149 pruned atom pairs is 0.357 angstroms; (across all 151 pairs:
0.438)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V24_holo_no_prot-coot-3.pdb,
chain A (#79), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.494 angstroms; (across all 151 pairs:
0.557)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V27_Mg-coot-2.pdb, chain A
(#50), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.544 angstroms; (across all 151 pairs:
0.594)  
  

> select #20-79/A

537720 atoms, 602280 bonds, 25020 residues, 60 models selected  

> color sel dim gray

> hide sel target a

> select #20-79/A:50,389,390

3960 atoms, 4380 bonds, 180 residues, 60 models selected  

> cartoon hide sel

> show sel target ab

> nucleotides sel atoms

> style nucleic & sel stick

Changed 3960 atom styles  

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> ui tool show "Color Actions"

> color sel cornflower blue

> hide #19#!1-18 target m

> select #20/C:1@O

1 atom, 1 residue, 1 model selected  

> select add #42/B:67@MG

2 atoms, 2 residues, 2 models selected  

> select add #61/B:65@MG

3 atoms, 3 residues, 3 models selected  

> select add #65/B:44@MG

4 atoms, 4 residues, 4 models selected  

> hide sel target a

> select #30/B:61@MG

1 atom, 1 residue, 1 model selected  

> select add #69/B:62@MG

2 atoms, 2 residues, 2 models selected  

> hide sel target a

> select #20-79/B

2199 atoms, 1 pseudobond, 2199 residues, 56 models selected  

> ui tool show "Selection Inspector"

> size sel atomRadius 0.7

Changed 2199 atom radii  

> select clear

> select #46/B:66@MG

1 atom, 1 residue, 1 model selected  

> select add #75/A:390@O3'

2 atoms, 2 residues, 2 models selected  

> distance #46/B:66@MG #75/A:390@O3'

Distance between V24_6sig.pdb #46/B MG 66 MG and V8_holo_no_prot_a-coot-4.pdb
#75/A A 390 O3': 5.502Å  

> close #42

> close #44

> close #46

> select #20-79/B

2062 atoms, 1 pseudobond, 2062 residues, 53 models selected  

> close #33

> close #63

> select #20-79/B:7

50 atoms, 50 residues, 50 models selected  

> select #75/C:7@MG

1 atom, 1 residue, 1 model selected  

> select add #69/B:7@MG

2 atoms, 2 residues, 2 models selected  

> select add #68/B:7@MG

3 atoms, 3 residues, 3 models selected  

> select add #55/B:7@MG

4 atoms, 4 residues, 4 models selected  

> select #20-79/B

1987 atoms, 1 pseudobond, 1987 residues, 51 models selected  

> select #20-79/C

187 atoms, 187 residues, 6 models selected  

> ui tool show "Selection Inspector"

> size sel atomRadius 0.7

Changed 187 atom radii  

> select #20-79/B:7

50 atoms, 50 residues, 50 models selected  

> ui tool show "Color Actions"

> color sel #941100ff

> select #20-79/C:7

5 atoms, 5 residues, 5 models selected  

> ui tool show "Color Actions"

> select #20-79/C:7

5 atoms, 5 residues, 5 models selected  

> ui tool show "Color Actions"

> color sel #4f8f00ff

> color sel #941100ff

> select #20-79/B

1987 atoms, 1 pseudobond, 1987 residues, 51 models selected  

> ui tool show "Color Actions"

> color sel forest green

> select #20-79/C

187 atoms, 187 residues, 6 models selected  

> ui tool show "Color Actions"

> color sel forest green

> select #20-79/C:7

5 atoms, 5 residues, 5 models selected  

> ui tool show "Color Actions"

> select #20-79/B:7

50 atoms, 50 residues, 50 models selected  

> ui tool show "Color Actions"

> color sel #945200ff

> color sel #941100ff

> select #20-79/C:7

5 atoms, 5 residues, 5 models selected  

> ui tool show "Color Actions"

> color sel #945200ff

> color sel #941100ff

> select clear

> select #20-79/B:57

21 atoms, 21 residues, 21 models selected  

> select #20-79/B:57,66

35 atoms, 35 residues, 25 models selected  

> select clear

> select #65/B:41@MG

1 atom, 1 residue, 1 model selected  

> select add #39/B:64@MG

2 atoms, 2 residues, 2 models selected  

> select add #41/B:62@MG

3 atoms, 3 residues, 3 models selected  

> select add #43/B:63@MG

4 atoms, 4 residues, 4 models selected  

> select subtract #43/B:63@MG

3 atoms, 3 residues, 3 models selected  

> select add #43/B:63@MG

4 atoms, 4 residues, 4 models selected  

> select subtract #41/B:62@MG

3 atoms, 3 residues, 3 models selected  

> select add #31/B:58@MG

4 atoms, 4 residues, 4 models selected  

> select add #30/B:57@MG

5 atoms, 5 residues, 5 models selected  

> select subtract #31/B:58@MG

4 atoms, 4 residues, 4 models selected  

> select subtract #65/B:41@MG

3 atoms, 3 residues, 3 models selected  

> select add #65/B:41@MG

4 atoms, 4 residues, 4 models selected  

> select add #31/B:58@MG

5 atoms, 5 residues, 5 models selected  

> select subtract #31/B:58@MG

4 atoms, 4 residues, 4 models selected  

> select subtract #39/B:64@MG

3 atoms, 3 residues, 3 models selected  

> select add #39/B:64@MG

4 atoms, 4 residues, 4 models selected  

> select add #38/B:61@MG

5 atoms, 5 residues, 5 models selected  

> select add #36/B:60@MG

6 atoms, 6 residues, 6 models selected  

> select subtract #43/B:63@MG

5 atoms, 5 residues, 5 models selected  

> select add #43/B:63@MG

6 atoms, 6 residues, 6 models selected  

> hide sel target a

> select #26/B:49@MG

1 atom, 1 residue, 1 model selected  

> select add #31/B:58@MG

2 atoms, 2 residues, 2 models selected  

> select add #41/B:62@MG

3 atoms, 3 residues, 3 models selected  

> select add #34/B:59@MG

4 atoms, 4 residues, 4 models selected  

> hide sel target a

> select #43/B:65@MG

1 atom, 1 residue, 1 model selected  

> select add #30/B:60@MG

2 atoms, 2 residues, 2 models selected  

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> select #50/B:64@MG

1 atom, 1 residue, 1 model selected  

> select add #35/B:62@MG

2 atoms, 2 residues, 2 models selected  

> select add #51/B:68@MG

3 atoms, 3 residues, 3 models selected  

> select add #69/B:57@MG

4 atoms, 4 residues, 4 models selected  

> select add #62/B:45@MG

5 atoms, 5 residues, 5 models selected  

> select add #64/B:42@MG

6 atoms, 6 residues, 6 models selected  

> select add #27/B:54@MG

7 atoms, 7 residues, 7 models selected  

> select add #59/B:66@MG

8 atoms, 8 residues, 8 models selected  

> hide sel target a

> show sel target ab

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> select #21/B:38@MG

1 atom, 1 residue, 1 model selected  

> select add #30/B:38@MG

2 atoms, 2 residues, 2 models selected  

> select add #26/B:38@MG

3 atoms, 3 residues, 3 models selected  

> select #26/B:38@MG

1 atom, 1 residue, 1 model selected  

> select add #59/B:64@MG

2 atoms, 2 residues, 2 models selected  

> distance #26/B:38@MG #59/B:64@MG

Distance between V7_Mg-coot-2.pdb #26/B MG 38 MG and V36_Mg-coot-1.pdb #59/B
MG 64 MG: 9.452Å  

> select #26/B:38@MG

1 atom, 1 residue, 1 model selected  

> select add #23/B:7@MG

2 atoms, 2 residues, 2 models selected  

> distance #26/B:38@MG #23/B:7@MG

Distance between V7_Mg-coot-2.pdb #26/B MG 38 MG and V4_Mg-coot-2.pdb #23/B MG
7 MG: 8.150Å  

> select #26/B:38@MG

1 atom, 1 residue, 1 model selected  

> select add #21/B:38@MG

2 atoms, 2 residues, 2 models selected  

> select add #30/B:38@MG

3 atoms, 3 residues, 3 models selected  

> hide sel target a

> select #36/B:38@MG

1 atom, 1 residue, 1 model selected  

> select add #59/B:38@MG

2 atoms, 2 residues, 2 models selected  

> hide sel target a

> select add #62/B:30@MG

3 atoms, 3 residues, 3 models selected  

> select #53/B:65@MG

1 atom, 1 residue, 1 model selected  

> select #75/A:390@O3'

1 atom, 1 residue, 1 model selected  

> select add #24/B:50@MG

2 atoms, 2 residues, 2 models selected  

> distance #75/A:390@O3' #24/B:50@MG

Distance between V8_holo_no_prot_a-coot-4.pdb #75/A A 390 O3' and V5_Mg-
coot-1.pdb #24/B MG 50 MG: 5.771Å  

> select #24/B:50@MG

1 atom, 1 residue, 1 model selected  

> select #47/B:66@MG

1 atom, 1 residue, 1 model selected  

> select add #34/B:61@MG

2 atoms, 2 residues, 2 models selected  

> select add #32/B:60@MG

3 atoms, 3 residues, 3 models selected  

> select add #24/B:50@MG

4 atoms, 4 residues, 4 models selected  

> select add #53/B:65@MG

5 atoms, 5 residues, 5 models selected  

> select add #48/B:69@MG

6 atoms, 6 residues, 6 models selected  

> select add #36/B:61@MG

7 atoms, 7 residues, 7 models selected  

> select #47/B:66@MG

1 atom, 1 residue, 1 model selected  

> select add #55/B:62@MG

2 atoms, 2 residues, 2 models selected  

> distance #47/B:66@MG #55/B:62@MG

Distance between V24_Mg-coot-6.pdb #47/B MG 66 MG and V32_Mg-coot-2.pdb #55/B
MG 62 MG: 5.257Å  

> save
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/apo_holo_analysis/ions/ions_apo_holo_new_core_aa_models.cxs

> select #43/B:65@MG

1 atom, 1 residue, 1 model selected  

> select add #58/B:4@MG

2 atoms, 2 residues, 2 models selected  

> distance #43/B:65@MG #58/B:4@MG

Distance between V22_Mg_real_space_refined_002-coot-1.pdb #43/B MG 65 MG and
V35_Mg-coot-2.pdb #58/B MG 4 MG: 9.512Å  

> select #43/B:65@MG

1 atom, 1 residue, 1 model selected  

> select add #30/B:60@MG

2 atoms, 2 residues, 2 models selected  

> hide sel target a

> save
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/apo_holo_analysis/ions/ions_apo_holo_new_core_aa_models.cxs

> select #59/B:64@MG

1 atom, 1 residue, 1 model selected  

> select clear

> select #48/B:30@MG

1 atom, 1 residue, 1 model selected  

> select add #75/C:7@MG

2 atoms, 2 residues, 2 models selected  

> distance #48/B:30@MG #75/C:7@MG

Distance between V25_Mg-coot-1.pdb #48/B MG 30 MG and V8_holo_no_prot_a-
coot-4.pdb #75/C MG 7 MG: 7.041Å  

> select #48/B:30@MG

1 atom, 1 residue, 1 model selected  

> select add #58/A:389@OP1

2 atoms, 2 residues, 2 models selected  

> distance #48/B:30@MG #58/A:389@OP1

Distance between V25_Mg-coot-1.pdb #48/B MG 30 MG and V35_Mg-coot-2.pdb #58/A
A 389 OP1: 2.362Å  

> select #69/B:30@MG

1 atom, 1 residue, 1 model selected  

> select add #65/B:30@MG

2 atoms, 2 residues, 2 models selected  

> select add #48/B:30@MG

3 atoms, 3 residues, 3 models selected  

> select add #41/B:30@MG

4 atoms, 4 residues, 4 models selected  

> select add #55/B:66@MG

5 atoms, 5 residues, 5 models selected  

> select add #50/B:30@MG

6 atoms, 6 residues, 6 models selected  

> color sel blue

> select clear

> select #39/B:65@MG

1 atom, 1 residue, 1 model selected  

> select add #75/A:390@O3'

2 atoms, 2 residues, 2 models selected  

> distance #39/B:65@MG #75/A:390@O3'

Distance between V19_Mg-coot-3.pdb #39/B MG 65 MG and V8_holo_no_prot_a-
coot-4.pdb #75/A A 390 O3': 4.560Å  

> select #28/B:40@MG

1 atom, 1 residue, 1 model selected  

> select #75/A:390@O3'

1 atom, 1 residue, 1 model selected  

> select add #72/B:40@MG

2 atoms, 2 residues, 2 models selected  

> distance #75/A:390@O3' #72/B:40@MG

Distance between V8_holo_no_prot_a-coot-4.pdb #75/A A 390 O3' and V48_Mg-
coot-1.pdb #72/B MG 40 MG: 5.512Å  

> select #20-79/B:40

33 atoms, 33 residues, 33 models selected  

> save
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/apo_holo_analysis/ions/ions_apo_holo_new_core_aa_models.cxs


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/apo_holo_analysis/ions/ions_apo_holo_new_core_aa_models.cxs

Log from Wed Sep 17 17:35:30 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3985_00049_volume_series/J3985_class_01_00049_volume.mrc

Opened J3985_class_01_00049_volume.mrc as #1, grid size 128,128,128, pixel
2.74, shown at level 0.0714, step 1, values float32  

> open
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3985_00049_volume_series/J3985_class_00_00049_volume.mrc

Opened J3985_class_00_00049_volume.mrc as #2, grid size 128,128,128, pixel
2.74, shown at level 0.0704, step 1, values float32  

> volume #2 level 0.1464

> volume #2 level 0.1878

> volume #1 level 0.1749

> volume #1 level 0.2362

> volume #2 level 0.2672

> volume #1 level 0.2324

> volume #1 level 0.2937

> volume #1 level 0.1634

> volume #1 level 0.1979

> volume #2 level 0.2879

> volume #1 level 0.2247

> volume #1 level 0.2055

> volume #2 level 0.3432

> volume #1 level 0.3014

> volume #1 level 0.1557

[Repeated 1 time(s)]

> ui tool show "Segment Map"

Select a density map in the Segment map field  
Segmenting J3985_class_01_00049_volume.mrc, density threshold 0.155709  
Showing 1 region surfaces  
187 watershed regions, grouped to 1 regions  
Showing J3985_class_01_00049_volume.seg - 1 regions, 1 surfaces  
Ungrouped to 3 regions  

> select #3.3

1 model selected  
Ungrouped to 8 regions  

> select #3.6

1 model selected  
Ungrouped to 5 regions  

> select #3.3

1 model selected  

> select add #3.14

2 models selected  

> select add #3.9

3 models selected  
Grouped 3 regions  
Ungrouped to 3 regions  

> select #3.6

1 model selected  
Ungrouped to 3 regions  

> select #3.3

1 model selected  
Ungrouped to 15 regions  

> select #3.31

1 model selected  

> select add #3.9

2 models selected  

> select add #3.14

3 models selected  
Grouped 3 regions  
Saving 1 regions to mrc file...  
Opened J3985_class_01_00049_volume_region_234.mrc as #4, grid size 21,17,18,
pixel 2.74, shown at step 1, values float32  
Wrote J3985_class_01_00049_volume_region_234.mrc  

> volume resample #4 onGrid 1

Invalid "onGrid" argument: invalid density maps specifier  

> volume resample #4 onGrid #1

Opened J3985_class_01_00049_volume_region_234.mrc resampled as #5, grid size
128,128,128, pixel 2.74, shown at step 1, values float32  

> hide #!3 models

> volume #5 level 0.2124

> volume #5 level 0.1251

> save
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3985_00049_volume_series/J3985_class_01_00049_volume_region_p.mrc
> models #5

> open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3986_006_volume_map.mrc

Opened cryosparc_P9_J3986_006_volume_map.mrc as #6, grid size 480,480,480,
pixel 0.732, shown at level 0.0101, step 2, values float32  

> volume #6 level 0.0249

> volume #6 level 0.01868

> volume #6 level 0.03345

> volume #!5-6 hide

> volume #1 level 0.2702

> volume #2 level 0.1264

> volume #1 level 0.1478

> volume #1 level 0.1123

> volume #2 level 0.1797

> volume #1 level 0.2623

> volume #2 level 0.3574

> volume #1 level 0.3294

> open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3984_007_volume_map.mrc

Opened cryosparc_P9_J3984_007_volume_map.mrc as #7, grid size 480,480,480,
pixel 0.732, shown at level 0.0104, step 2, values float32  

> volume #!1,7 hide

> volume #7 level 0.02771

> volume #7 level 0.04405

> volume #7 level 0.03924

> volume #7 level 0.04789

> volume #7 level 0.0575

> open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3983_007_volume_map.mrc

Opened cryosparc_P9_J3983_007_volume_map.mrc as #8, grid size 480,480,480,
pixel 0.732, shown at level 0.0105, step 2, values float32  

> volume #8 level 0.0575

> volume #8 level 0.04195

> volume #7 level 0.03636

> select add #7

3 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #3.3,0.99455,-0.074938,-0.072552,27.272,0.072407,0.99669,-0.036905,-6.1312,0.075078,0.03145,0.99668,-18.795,#7,0.99455,-0.074938,-0.072552,27.272,0.072407,0.99669,-0.036905,-6.1312,0.075078,0.03145,0.99668,-18.795

> view matrix models
> #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93,#7,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93

> fitmap #7 inMap #8

Fit map cryosparc_P9_J3984_007_volume_map.mrc in map
cryosparc_P9_J3983_007_volume_map.mrc using 49963 points  
correlation = 0.9959, correlation about mean = 0.984, overlap = 500.7  
steps = 380, shift = 16.1, angle = 34.3 degrees  
  
Position of cryosparc_P9_J3984_007_volume_map.mrc (#7) relative to
cryosparc_P9_J3983_007_volume_map.mrc (#8) coordinates:  
Matrix rotation and translation  
-0.72583440 0.68279829 -0.08337219 201.41842056  
-0.29586248 -0.41930957 -0.85828018 446.74544623  
-0.62099100 -0.59830258 0.50636370 306.03816839  
Axis 0.22676305 0.46893301 -0.85362776  
Axis point 224.32984314 270.00684921 0.00000000  
Rotation angle (degrees) 145.02379031  
Shift along axis -6.07473264  
  

> fitmap #7 inMap #8

Fit map cryosparc_P9_J3984_007_volume_map.mrc in map
cryosparc_P9_J3983_007_volume_map.mrc using 49963 points  
correlation = 0.9959, correlation about mean = 0.984, overlap = 500.7  
steps = 64, shift = 0.012, angle = 0.00824 degrees  
  
Position of cryosparc_P9_J3984_007_volume_map.mrc (#7) relative to
cryosparc_P9_J3983_007_volume_map.mrc (#8) coordinates:  
Matrix rotation and translation  
-0.72583244 0.68280184 -0.08336017 201.41856784  
-0.29596038 -0.41938679 -0.85820870 446.76271306  
-0.62094664 -0.59824441 0.50648682 306.00978970  
Axis 0.22673791 0.46887682 -0.85366530  
Axis point 224.32617617 269.99245085 0.00000000  
Rotation angle (degrees) 145.02139829  
Shift along axis -6.08403693  
  

> fitmap #7 inMap #8

Fit map cryosparc_P9_J3984_007_volume_map.mrc in map
cryosparc_P9_J3983_007_volume_map.mrc using 49963 points  
correlation = 0.9959, correlation about mean = 0.984, overlap = 500.7  
steps = 44, shift = 0.0118, angle = 0.00629 degrees  
  
Position of cryosparc_P9_J3984_007_volume_map.mrc (#7) relative to
cryosparc_P9_J3983_007_volume_map.mrc (#8) coordinates:  
Matrix rotation and translation  
-0.72584163 0.68278694 -0.08340211 201.42434440  
-0.29586571 -0.41935773 -0.85825554 446.75301724  
-0.62098100 -0.59828178 0.50640054 306.02837341  
Axis 0.22676494 0.46890903 -0.85364043  
Axis point 224.32912008 270.00287478 0.00000000  
Rotation angle (degrees) 145.02471726  
Shift along axis -6.07568669  
  

> fitmap #7 inMap #8

Fit map cryosparc_P9_J3984_007_volume_map.mrc in map
cryosparc_P9_J3983_007_volume_map.mrc using 49963 points  
correlation = 0.9959, correlation about mean = 0.984, overlap = 500.7  
steps = 100, shift = 0.0117, angle = 0.00919 degrees  
  
Position of cryosparc_P9_J3984_007_volume_map.mrc (#7) relative to
cryosparc_P9_J3983_007_volume_map.mrc (#8) coordinates:  
Matrix rotation and translation  
-0.72585579 0.68276216 -0.08348176 201.44447216  
-0.29589017 -0.41949591 -0.85817958 446.76049346  
-0.62095280 -0.59821318 0.50651615 305.99878042  
Axis 0.22676890 0.46883644 -0.85367925  
Axis point 224.32788267 269.98130269 0.00000000  
Rotation angle (degrees) 145.02655337  
Shift along axis -6.08586737  
  

> volume #8 level 0.0364

> select subtract #7

1 model selected  

> view matrix models
> #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93

> volume #7 level 0.06423

> view matrix models
> #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93

> volume #7 level 0.02003

> volume #8 level 0.02571

> volume #8 level 0.04417

> open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3969_006_volume_map.mrc

Opened cryosparc_P9_J3969_006_volume_map.mrc as #9, grid size 480,480,480,
pixel 0.732, shown at level 0.0103, step 2, values float32  

> volume #9 level 0.03176

> volume #9 level 0.01519

> open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3951_008_volume_map.mrc

Opened cryosparc_P9_J3951_008_volume_map.mrc as #10, grid size 480,480,480,
pixel 0.732, shown at level 0.0114, step 2, values float32  

> volume #!8,10 hide

> volume #10 level 0.03828

> volume #10 level 0.02869

> volume #10 level 0.04979

> fitmap #1 inMap #10

Fit map J3985_class_01_00049_volume.mrc in map
cryosparc_P9_J3951_008_volume_map.mrc using 6629 points  
correlation = 0.8689, correlation about mean = 0.602, overlap = 377  
steps = 96, shift = 1.6, angle = 4.19 degrees  
  
Position of J3985_class_01_00049_volume.mrc (#1) relative to
cryosparc_P9_J3951_008_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.99743315 -0.00176327 -0.07158214 11.61334330  
0.00282388 0.99988770 0.01471808 -3.39292521  
0.07154815 -0.01488244 0.99732611 -10.23271671  
Axis -0.20242295 -0.97879565 0.03136921  
Axis point 149.23497483 0.00000000 158.72238428  
Rotation angle (degrees) 4.19295196  
Shift along axis 0.64918094  
  

> fitmap #1 inMap #10

Fit map J3985_class_01_00049_volume.mrc in map
cryosparc_P9_J3951_008_volume_map.mrc using 6629 points  
correlation = 0.8688, correlation about mean = 0.6019, overlap = 377  
steps = 40, shift = 0.0111, angle = 0.00583 degrees  
  
Position of J3985_class_01_00049_volume.mrc (#1) relative to
cryosparc_P9_J3951_008_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.99743292 -0.00175838 -0.07158540 11.60987325  
0.00281177 0.99988921 0.01461711 -3.38346500  
0.07155176 -0.01478087 0.99732736 -10.24684374  
Axis -0.20108561 -0.97907475 0.03126035  
Axis point 149.42296601 0.00000000 158.67147531  
Rotation angle (degrees) 4.19195597  
Shift along axis 0.65776684  
  

> fitmap #1 inMap #10

Fit map J3985_class_01_00049_volume.mrc in map
cryosparc_P9_J3951_008_volume_map.mrc using 6629 points  
correlation = 0.8688, correlation about mean = 0.6019, overlap = 377  
steps = 60, shift = 0.00202, angle = 0.00304 degrees  
  
Position of J3985_class_01_00049_volume.mrc (#1) relative to
cryosparc_P9_J3951_008_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.99743293 -0.00175093 -0.07158545 11.60870841  
0.00280811 0.99988844 0.01467011 -3.38985788  
0.07155178 -0.01483347 0.99732658 -10.23757914  
Axis -0.20177899 -0.97893465 0.03117985  
Axis point 149.29375605 0.00000000 158.66352892  
Rotation angle (degrees) 4.19255884  
Shift along axis 0.65684980  
  

> fitmap #1 inMap #10

Fit map J3985_class_01_00049_volume.mrc in map
cryosparc_P9_J3951_008_volume_map.mrc using 6629 points  
correlation = 0.8688, correlation about mean = 0.6019, overlap = 377  
steps = 96, shift = 0.002, angle = 0.00324 degrees  
  
Position of J3985_class_01_00049_volume.mrc (#1) relative to
cryosparc_P9_J3951_008_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.99743159 -0.00171901 -0.07160488 11.60617014  
0.00277352 0.99988913 0.01463001 -3.37850973  
0.07157180 -0.01479103 0.99732578 -10.24880751  
Axis -0.20118700 -0.97907100 0.03072081  
Axis point 149.40364660 0.00000000 158.57590880  
Rotation angle (degrees) 4.19313151  
Shift along axis 0.65793867  
  

> open
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3989_00048_volume_series/J3989_class_01_00048_volume.mrc

Opened J3989_class_01_00048_volume.mrc as #11, grid size 128,128,128, pixel
2.74, shown at level 0.0696, step 1, values float32  

> open
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3989_00048_volume_series/J3989_class_00_00048_volume.mrc

Opened J3989_class_00_00048_volume.mrc as #12, grid size 128,128,128, pixel
2.74, shown at level 0.0695, step 1, values float32  

> volume #!1,10-12 hide

> volume #12 level 0.1515

> volume #11 level 0.1326

> volume #11 level 0.1548

> volume #1 level 0.211

> volume #2 level 0.1832

> volume #!2 hide

> open
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3968_00116_volume_series/J3968_class_01_00116_volume.mrc

Opened J3968_class_01_00116_volume.mrc as #13, grid size 144,144,144, pixel
2.75, shown at level 0.0545, step 1, values float32  

> open
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3968_00116_volume_series/J3968_class_00_00116_volume.mrc

Opened J3968_class_00_00116_volume.mrc as #14, grid size 144,144,144, pixel
2.75, shown at level 0.0495, step 1, values float32  

> volume #14 level 0.115

> volume #13 level 0.1179

> select add #13

3 models selected  

> hide #!14 models

> fitmap #13 inMap #11

Fit map J3968_class_01_00116_volume.mrc in map J3989_class_01_00048_volume.mrc
using 15819 points  
correlation = 0.8706, correlation about mean = 0.722, overlap = 2919  
steps = 140, shift = 37.7, angle = 1.37 degrees  
  
Position of J3968_class_01_00116_volume.mrc (#13) relative to
J3989_class_01_00048_volume.mrc (#11) coordinates:  
Matrix rotation and translation  
0.99971437 0.01959626 0.01368115 -28.66197852  
-0.01958627 0.99980780 -0.00086396 -16.84931847  
-0.01369545 0.00059576 0.99990604 -19.58306288  
Axis 0.03052447 0.57247681 -0.81935252  
Axis point -1036.02962297 1456.12966984 0.00000000  
Rotation angle (degrees) 1.37011058  
Shift along axis 5.52469615  
  

> fitmap #13 inMap #11

Fit map J3968_class_01_00116_volume.mrc in map J3989_class_01_00048_volume.mrc
using 15819 points  
correlation = 0.8705, correlation about mean = 0.7217, overlap = 2919  
steps = 56, shift = 0.023, angle = 0.0138 degrees  
  
Position of J3968_class_01_00116_volume.mrc (#13) relative to
J3989_class_01_00048_volume.mrc (#11) coordinates:  
Matrix rotation and translation  
0.99971346 0.01976263 0.01350659 -28.68065746  
-0.01975270 0.99980452 -0.00086839 -16.82188386  
-0.01352112 0.00060135 0.99990840 -19.61515682  
Axis 0.03068551 0.56428859 -0.82500714  
Axis point -1031.91078715 1445.31671200 0.00000000  
Rotation angle (degrees) 1.37227811  
Shift along axis 5.81016679  
  

> fitmap #11 inMap #14

Fit map J3989_class_01_00048_volume.mrc in map J3968_class_00_00116_volume.mrc
using 11649 points  
correlation = 0.8966, correlation about mean = 0.7157, overlap = 2894  
steps = 124, shift = 38, angle = 1.45 degrees  
  
Position of J3989_class_01_00048_volume.mrc (#11) relative to
J3968_class_00_00116_volume.mrc (#14) coordinates:  
Matrix rotation and translation  
0.99969266 -0.02253533 -0.01033133 28.08037343  
0.02259070 0.99973088 0.00527456 16.14208619  
0.01020969 -0.00550634 0.99993272 21.38876177  
Axis -0.21247458 -0.40483111 0.88936287  
Axis point -815.69812369 1318.66977759 0.00000000  
Rotation angle (degrees) 1.45374188  
Shift along axis 6.52118636  
  

> fitmap #11 inMap #14

Fit map J3989_class_01_00048_volume.mrc in map J3968_class_00_00116_volume.mrc
using 11649 points  
correlation = 0.8967, correlation about mean = 0.7151, overlap = 2889  
steps = 80, shift = 0.042, angle = 0.00904 degrees  
  
Position of J3989_class_01_00048_volume.mrc (#11) relative to
J3968_class_00_00116_volume.mrc (#14) coordinates:  
Matrix rotation and translation  
0.99969400 -0.02251644 -0.01024267 28.07371662  
0.02257002 0.99973202 0.00514573 16.13692320  
0.01012406 -0.00537533 0.99993430 21.40764237  
Axis -0.20801043 -0.40266782 0.89139794  
Axis point -819.63745883 1320.26275326 0.00000000  
Rotation angle (degrees) 1.44915013  
Shift along axis 6.74528284  
  

> fitmap #11 inMap #14

Fit map J3989_class_01_00048_volume.mrc in map J3968_class_00_00116_volume.mrc
using 11649 points  
correlation = 0.8965, correlation about mean = 0.7152, overlap = 2893  
steps = 80, shift = 0.0478, angle = 0.0308 degrees  
  
Position of J3989_class_01_00048_volume.mrc (#11) relative to
J3968_class_00_00116_volume.mrc (#14) coordinates:  
Matrix rotation and translation  
0.99968804 -0.02285456 -0.01007459 28.12280975  
0.02291102 0.99972224 0.00552539 16.05278061  
0.00994551 -0.00575449 0.99993398 21.48943495  
Axis -0.22026445 -0.39093637 0.89367350  
Axis point -799.73209073 1306.33286302 0.00000000  
Rotation angle (degrees) 1.46723678  
Shift along axis 6.73446774  
  

> fitmap #11 inMap #14

Fit map J3989_class_01_00048_volume.mrc in map J3968_class_00_00116_volume.mrc
using 11649 points  
correlation = 0.8965, correlation about mean = 0.7151, overlap = 2893  
steps = 64, shift = 0.00592, angle = 0.0116 degrees  
  
Position of J3989_class_01_00048_volume.mrc (#11) relative to
J3968_class_00_00116_volume.mrc (#14) coordinates:  
Matrix rotation and translation  
0.99969172 -0.02267013 -0.01012540 28.09508155  
0.02272756 0.99972605 0.00559283 16.07389740  
0.00999584 -0.00582123 0.99993310 21.49281283  
Axis -0.22401656 -0.39490657 0.89099123  
Axis point -804.48634434 1314.55289352 0.00000000  
Rotation angle (degrees) 1.45982216  
Shift along axis 6.50845650  
  

> hide #!11 models

> select subtract #13

1 model selected  

> volume #14 level 0.2241

> volume #14 level 0.06262

> volume #14 level 0.2241

> volume #14 level 0.4248

> volume #14 level 0.115

> volume #14 level 0.1717

> volume #14 level 0.211

> volume #14 level 0.1237

> volume #14 level 0.06698

> volume #14 level 0.2764

> volume #14 level 0.2241

> volume #14 level 0.2197

> volume #14 level 0.2808

> view matrix models
> #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93

> volume #14 level 0.1673

> volume #14 level 0.211

> view matrix models
> #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93

[Repeated 2 time(s)]

> volume #14 level 0.09752

> volume #14 level 0.1804

> volume #14 level 0.307

> volume #14 level 0.08007

> volume #14 level 0.1062

> view matrix models
> #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93

[Repeated 1 time(s)]

> volume #14 level 0.1542

> volume #14 level 0.1979

> view matrix models
> #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93

> volume #14 level 0.1499

> volume #14 level 0.2066

> volume #14 level 0.1019

> volume #14 level 0.1542

> volume #14 level 0.2022

> view matrix models
> #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93

> volume #14 level 0.115

> volume #14 level 0.403

> volume #14 level 0.1019

> open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3967_007_volume_map.mrc

Opened cryosparc_P9_J3967_007_volume_map.mrc as #15, grid size 324,324,324,
pixel 1.22, shown at level 0.0302, step 2, values float32  

> volume #15 level 0.08332

> volume #15 level 0.101

> volume #15 level 0.08996

> volume #15 level 0.07669

> volume #15 level 0.09438

> volume #15 level 0.163

> volume #15 level 0.1696

[Repeated 1 time(s)]Segmenting cryosparc_P9_J3967_007_volume_map.mrc, density
threshold 0.169599  
Showing 17 region surfaces  
1009 watershed regions, grouped to 17 regions  
Showing cryosparc_P9_J3967_007_volume_map.seg - 17 regions, 17 surfaces  
Segmenting cryosparc_P9_J3967_007_volume_map.mrc, density threshold 0.169599  
Showing 17 region surfaces  
1009 watershed regions, grouped to 17 regions  
Showing cryosparc_P9_J3967_007_volume_map.seg - 17 regions, 17 surfaces  

> select #3.17

1 model selected  
Deleted 1 regions  

> select #3.3

1 model selected  

> select clear

> select #3.1

1 model selected  

> select add #3.7

2 models selected  

> select add #3.8

3 models selected  

> select add #3.12

4 models selected  

> select add #3.10

5 models selected  

> select add #3.16

6 models selected  

> select add #3.2

7 models selected  

> select add #3.3

8 models selected  

> select add #3.11

9 models selected  

> select add #3.6

10 models selected  

> select add #3.4

11 models selected  

> select add #3.5

12 models selected  

> select subtract #3.2

11 models selected  

> select add #3.9

12 models selected  

> select clear

Drag select of 1359, 48002 of 48056 triangles, 1356, 1362, 1341, 1360, 1345,
1335, 1339, 1350, 1357, 1358, 1344, 1347, 1281, 1361, 1338, 15
cryosparc_P9_J3967_007_volume_map.mrc  

> view matrix models
> #15,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.1,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.2,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.3,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.4,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.5,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.6,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.7,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.8,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.9,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.10,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.11,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.12,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.13,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.14,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.15,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.16,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796

Saving 16 regions to mrc file...  
Opened cryosparc_P9_J3967_007_volume_map_16_regions.mrc as #16, grid size
73,125,114, pixel 1.22, shown at step 1, values float32  
Wrote cryosparc_P9_J3967_007_volume_map_16_regions.mrc  

> volume resample #16 onGrid #15

Opened cryosparc_P9_J3967_007_volume_map_16_regions.mrc resampled as #17, grid
size 324,324,324, pixel 1.22, shown at step 1, values float32  

> hide #!3 models

> volume #17 level 0.09743

> save
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3967_007_volume_map_16_regions.mrc
> models #17

> volume #16 level 0.296

> volume #16 level 0.2176

> volume #16 level 0.2393

> close #16

> close #17

> volume #15 level 0.06784

> volume #15 level 0.03687

> volume #15 level 0.0966

> volume #15 level 0.08111

> volume #15 level 0.1254

> view matrix models
> #15,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.1,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.2,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.3,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.4,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.5,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.6,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.7,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.8,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.9,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.10,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.11,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.12,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.13,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.14,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.15,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.16,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69

> close session

> open
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3977_00142_volumes/J3977_class_03_00142_volume.mrc

Opened J3977_class_03_00142_volume.mrc as #1, grid size 128,128,128, pixel
3.09, shown at level 0.0569, step 1, values float32  

> open
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3977_00142_volumes/J3977_class_02_00142_volume.mrc

Opened J3977_class_02_00142_volume.mrc as #2, grid size 128,128,128, pixel
3.09, shown at level 0.0652, step 1, values float32  

> open
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3977_00142_volumes/J3977_class_01_00142_volume.mrc

Opened J3977_class_01_00142_volume.mrc as #3, grid size 128,128,128, pixel
3.09, shown at level 0.0644, step 1, values float32  

> open
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3977_00142_volumes/J3977_class_00_00142_volume.mrc

Opened J3977_class_00_00142_volume.mrc as #4, grid size 128,128,128, pixel
3.09, shown at level 0.0511, step 1, values float32  

> surface dust #1 size 30.9

> surface dust #2 size 30.9

> surface dust #3 size 30.9

> surface dust #4 size 30.9

> volume #!1-2,4 hide

> select add #4

2 models selected  

> view matrix models
> #4,0.94781,0.16804,0.27096,-68.241,-0.31283,0.32602,0.8921,34.283,0.061569,-0.93031,0.36157,273.55

> view matrix models
> #4,0.95967,0.13122,0.24861,-59.846,-0.27903,0.33713,0.89916,24.083,0.034174,-0.93227,0.36015,279.75

> view matrix models
> #4,0.81403,-0.58022,0.026318,142.13,0.23948,0.37658,0.89489,-88.181,-0.52915,-0.72217,0.4455,340.15

> volume #3 level 0.08997

> volume #3 level 0.1412

> volume #4 level 0.1357

> view matrix models
> #4,-0.98182,-0.15393,0.11102,400.77,-0.16014,0.98586,-0.049341,48.503,-0.10186,-0.066224,-0.99259,395.11

> view matrix models
> #4,-0.88503,0.34552,0.312,251.01,0.33497,0.93805,-0.088657,-33.002,-0.3233,0.026046,-0.94594,412.92

> volume #4 level 0.3894

> volume #4 z flip

Expected a keyword  

> volume #4 zflip

Expected a keyword  

> volume #4 flipNormals

Missing "flipNormals" keyword's argument  

> volume flip #4

Opened J3977_class_00_00142_volume.mrc z flip as #5, grid size 128,128,128,
pixel 3.09, shown at step 1, values float32  

> select #5

2 models selected  

> view matrix models
> #5,-0.85933,0.30635,0.40953,234.55,-0.2375,0.47014,-0.85004,313.88,-0.45294,-0.82772,-0.33125,480.43

> fitmap #5 inMap #3

Fit map J3977_class_00_00142_volume.mrc z flip in map
J3977_class_01_00142_volume.mrc using 4563 points  
correlation = 0.9699, correlation about mean = 0.7826, overlap = 2457  
steps = 132, shift = 31.6, angle = 38.4 degrees  
  
Position of J3977_class_00_00142_volume.mrc z flip (#5) relative to
J3977_class_01_00142_volume.mrc (#3) coordinates:  
Matrix rotation and translation  
-0.99116610 0.00155516 -0.13261718 420.28508914  
0.12896783 0.24454249 -0.96102354 304.65893499  
0.03093599 -0.96963731 -0.24258280 429.65932782  
Axis -0.04151142 -0.78819365 0.61402571  
Axis point 188.06887356 0.00000000 347.37550767  
Rotation angle (degrees) 174.04473730  
Shift along axis 6.24500964  
  

> fitmap #5 inMap #3

Fit map J3977_class_00_00142_volume.mrc z flip in map
J3977_class_01_00142_volume.mrc using 4563 points  
correlation = 0.9699, correlation about mean = 0.7826, overlap = 2457  
steps = 48, shift = 0.0213, angle = 0.0281 degrees  
  
Position of J3977_class_00_00142_volume.mrc z flip (#5) relative to
J3977_class_01_00142_volume.mrc (#3) coordinates:  
Matrix rotation and translation  
-0.99117083 0.00165958 -0.13258052 420.24478315  
0.12894289 0.24500496 -0.96090909 304.53529817  
0.03088818 -0.96952039 -0.24305576 429.72894017  
Axis -0.04152874 -0.78834163 0.61383453  
Axis point 188.06053369 0.00000000 347.28922017  
Rotation angle (degrees) 174.04894559  
Shift along axis 6.25237502  
  

> volume #3 level 0.6852

> volume #5 level 0.188

> volume #3 level 0.1028

> volume #3 level 0.138

> volume #5 level 0.1598

> volume #5 level 0.1679

> volume #3 level 0.07077

> volume #3 level 0.1988

> volume #5 level 0.2806

> volume #1 level 0.2265

> fitmap #5 inMap #1

Fit map J3977_class_00_00142_volume.mrc z flip in map
J3977_class_03_00142_volume.mrc using 6115 points  
correlation = 0.9725, correlation about mean = 0.8601, overlap = 2909  
steps = 84, shift = 2.02, angle = 4.3 degrees  
  
Position of J3977_class_00_00142_volume.mrc z flip (#5) relative to
J3977_class_03_00142_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.99754203 0.02498920 -0.06546303 405.36740821  
0.06977180 0.26807185 -0.96086906 311.85792420  
-0.00646256 -0.96307476 -0.26915648 438.89272991  
Axis -0.02976493 -0.79618479 0.60432096  
Axis point 191.78070263 0.00000000 342.51916349  
Rotation angle (degrees) 177.87659093  
Shift along axis 4.86980674  
  

> fitmap #5 inMap #1

Fit map J3977_class_00_00142_volume.mrc z flip in map
J3977_class_03_00142_volume.mrc using 6115 points  
correlation = 0.9725, correlation about mean = 0.8601, overlap = 2909  
steps = 44, shift = 0.0143, angle = 0.0162 degrees  
  
Position of J3977_class_00_00142_volume.mrc z flip (#5) relative to
J3977_class_03_00142_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.99754942 0.02519611 -0.06527087 405.29719322  
0.06964248 0.26808225 -0.96087554 311.87541512  
-0.00671237 -0.96306647 -0.26918001 438.93275976  
Axis -0.02978898 -0.79618924 0.60431392  
Axis point 191.77820368 0.00000000 342.50753611  
Rotation angle (degrees) 177.89251633  
Shift along axis 4.86793646  
  

> volume #1 level 0.3043

> volume #1 level 0.2513

> volume sel hide

> volume #1 level 0.1453

> volume #4 level 0.1961

> close #4

> volume #5 level 0.2122

> volume #1 level 0.2053

> fitmap #5 inMap #1

Fit map J3977_class_00_00142_volume.mrc z flip in map
J3977_class_03_00142_volume.mrc using 7583 points  
correlation = 0.9685, correlation about mean = 0.8754, overlap = 2994  
steps = 48, shift = 0.038, angle = 0.0347 degrees  
  
Position of J3977_class_00_00142_volume.mrc z flip (#5) relative to
J3977_class_03_00142_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.99750974 0.02523858 -0.06585823 405.37295159  
0.07022047 0.26819842 -0.96080105 311.75529366  
-0.00658618 -0.96303302 -0.26930280 438.93804803  
Axis -0.02998281 -0.79622383 0.60425876  
Axis point 191.71948602 0.00000000 342.50624022  
Rotation angle (degrees) 177.86691692  
Shift along axis 4.85094606  
  

> fitmap #5 inMap #1

Fit map J3977_class_00_00142_volume.mrc z flip in map
J3977_class_03_00142_volume.mrc using 7583 points  
correlation = 0.9684, correlation about mean = 0.8752, overlap = 2994  
steps = 44, shift = 0.0584, angle = 0.026 degrees  
  
Position of J3977_class_00_00142_volume.mrc z flip (#5) relative to
J3977_class_03_00142_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.99752439 0.02490787 -0.06576214 405.45522347  
0.07003701 0.26791788 -0.96089271 311.91208460  
-0.00631494 -0.96311971 -0.26899910 438.84730228  
Axis -0.02982470 -0.79613522 0.60438332  
Axis point 191.77259653 0.00000000 342.57395662  
Rotation angle (degrees) 177.86037271  
Shift along axis 4.81521528  
  

> select subtract #5

Nothing selected  

> show #!5 models

> volume #5 level 0.2525

> hide #!5 models

> show #!1 models

> volume #1 level 0.2795

> volume #1 level 0.276

> volume #1 level 0.08519

> volume #1 level 0.1665

> volume #2 level 0.1703

> volume #2 level 0.1327

> volume #2 level 0.1928

> volume #1 level 0.223

> fitmap #1 inMap #2

Fit map J3977_class_03_00142_volume.mrc in map J3977_class_02_00142_volume.mrc
using 7452 points  
correlation = 0.9571, correlation about mean = 0.8286, overlap = 2948  
steps = 84, shift = 1.2, angle = 2.65 degrees  
  
Position of J3977_class_03_00142_volume.mrc (#1) relative to
J3977_class_02_00142_volume.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99892948 -0.04344038 -0.01590040 11.73510950  
0.04345212 0.99905543 0.00039400 -9.71668965  
0.01586826 -0.00108448 0.99987350 -3.49169470  
Axis -0.01597843 -0.34333482 0.93907715  
Axis point 230.39658326 264.41720009 0.00000000  
Rotation angle (degrees) 2.65172634  
Shift along axis -0.13040143  
  

> hide #!1 models

> volume #2 level 0.08769

> volume #2 level 0.0539

> volume #2 level 0.03889

> volume #3 level 0.03877

> volume #3 level 0.08037

> volume #2 level 0.0539

> volume #2 level 0.06517

> volume #2 level 0.07267

> volume #2 level 0.07643

> volume #2 level 0.08018

> volume #!2 hide

> volume #5 level 0.06724

> volume #5 level 0.1156

> volume #5 level 0.5102

> volume #5 level 0.3088

> volume #5 level 0.2364

> volume #5 level 0.2202

> volume #5 level 0.2162

> volume #5 level 0.2122

[Repeated 1 time(s)]

> volume #5 level 0.2082

> volume #5 level 0.2041

[Repeated 1 time(s)]

> volume #5 level 0.2001

> volume #5 level 0.1961

[Repeated 1 time(s)]

> volume #5 level 0.1921

> volume #5 level 0.188

> volume #5 level 0.184

> volume #5 level 0.18

> volume #5 level 0.176

> volume #5 level 0.1719

> volume #5 level 0.1679

> volume #5 level 0.1639

> volume #5 level 0.1598

> volume #5 level 0.1558

> volume #5 level 0.1518

[Repeated 1 time(s)]

> volume #5 level 0.1478

> volume #5 level 0.1437

> volume #5 level 0.1397

> open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3954_006_volume_map.mrc

Opened cryosparc_P9_J3954_006_volume_map.mrc as #4, grid size 324,324,324,
pixel 1.22, shown at level 0.0183, step 2, values float32  

> volume #!4-5 hide

> volume #4 level 0.06737

> volume #4 level 0.08168

> volume #4 level 0.03262

> volume #4 level 0.0551

> volume #4 level 0.0735

> ui tool show Segmentations

> ui view fourup

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen  
self._update_position_label_text()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'  
  
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen  
self._update_position_label_text()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'  
  
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen  
self._update_position_label_text()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'  
  
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> close session

> open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3954_006_volume_map.mrc

Opened cryosparc_P9_J3954_006_volume_map.mrc as #1, grid size 324,324,324,
pixel 1.22, shown at level 0.0183, step 2, values float32  

> volume #1 level 0.03022

> ui tool show "Segment Map"

> volume #1 level 0.06089

Segmenting cryosparc_P9_J3954_006_volume_map.mrc, density threshold 0.060885  
Showing 17 region surfaces  
1782 watershed regions, grouped to 17 regions  
Showing cryosparc_P9_J3954_006_volume_map.seg - 17 regions, 17 surfaces  

> select #2.4

1 model selected  
Saving 1 regions to mrc file...  
Opened cryosparc_P9_J3954_006_volume_map_region_2128.mrc as #3, grid size
42,45,72, pixel 1.22, shown at step 1, values float32  
Wrote cryosparc_P9_J3954_006_volume_map_region_2128.mrc  

> volume resample #3 onGrid #1

Opened cryosparc_P9_J3954_006_volume_map_region_2128.mrc resampled as #4, grid
size 324,324,324, pixel 1.22, shown at step 1, values float32  

> save
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3954_006_volume_map_region_2128.mrc
> models #4

> volume #1 level 0.07315

> close session

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V2_holo-
> coot-2.pdb

Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V2_holo-
coot-2.pdb  
---  
warnings | Duplicate atom serial number found: 8964  
Duplicate atom serial number found: 8965  
Duplicate atom serial number found: 8966  
Duplicate atom serial number found: 8967  
Duplicate atom serial number found: 8968  
26 messages similar to the above omitted  
  
Chain information for V2_holo-coot-2.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V3_holo-
> coot-2.pdb

Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V3_holo-
coot-2.pdb  
---  
warnings | Duplicate atom serial number found: 8964  
Duplicate atom serial number found: 8965  
Duplicate atom serial number found: 8966  
Duplicate atom serial number found: 8967  
Duplicate atom serial number found: 8968  
26 messages similar to the above omitted  
  
Chain information for V3_holo-coot-2.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V4_holo-
> coot-3.pdb

Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V4_holo-
coot-3.pdb  
---  
warnings | Duplicate atom serial number found: 8965  
Duplicate atom serial number found: 8966  
Duplicate atom serial number found: 8967  
Duplicate atom serial number found: 8968  
Duplicate atom serial number found: 8969  
30 messages similar to the above omitted  
  
Chain information for V4_holo-coot-3.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V5_holo-
> coot-1.pdb

Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V5_holo-
coot-1.pdb  
---  
warnings | Duplicate atom serial number found: 8965  
Duplicate atom serial number found: 8966  
Duplicate atom serial number found: 8967  
Duplicate atom serial number found: 8968  
Duplicate atom serial number found: 8969  
17 messages similar to the above omitted  
  
Chain information for V5_holo-coot-1.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V6_holo-
> coot-1.pdb

Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V6_holo-
coot-1.pdb  
---  
warnings | Duplicate atom serial number found: 8965  
Duplicate atom serial number found: 8966  
Duplicate atom serial number found: 8967  
Duplicate atom serial number found: 8968  
Duplicate atom serial number found: 8969  
20 messages similar to the above omitted  
  
Chain information for V6_holo-coot-1.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V7_holo-
> coot-2.pdb

Chain information for V7_holo-coot-2.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V9_holo-
> coot-0.pdb

Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V9_holo-
coot-0.pdb  
---  
warnings | Duplicate atom serial number found: 8965  
Duplicate atom serial number found: 8966  
Duplicate atom serial number found: 8967  
Duplicate atom serial number found: 8968  
Duplicate atom serial number found: 8969  
24 messages similar to the above omitted  
  
Chain information for V9_holo-coot-0.pdb #7  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V10_holo-
> coot-1.pdb

Chain information for V10_holo-coot-1.pdb #8  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V11_holo-
> coot-1.pdb

Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V11_holo-
coot-1.pdb  
---  
warnings | Duplicate atom serial number found: 8965  
Duplicate atom serial number found: 8966  
Duplicate atom serial number found: 8967  
Duplicate atom serial number found: 8968  
Duplicate atom serial number found: 8969  
29 messages similar to the above omitted  
  
Chain information for V11_holo-coot-1.pdb #9  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V12_holo-
> coot-3.pdb

Chain information for V12_holo-coot-3.pdb #10  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V14_holo-
> coot-1.pdb

Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V14_holo-
coot-1.pdb  
---  
warnings | Duplicate atom serial number found: 8964  
Duplicate atom serial number found: 8965  
Duplicate atom serial number found: 8966  
Duplicate atom serial number found: 8967  
Duplicate atom serial number found: 8968  
28 messages similar to the above omitted  
  
Chain information for V14_holo-coot-1.pdb #11  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V15_holo-
> coot-1.pdb

Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V15_holo-
coot-1.pdb  
---  
warnings | Duplicate atom serial number found: 8965  
Duplicate atom serial number found: 8966  
Duplicate atom serial number found: 8968  
Duplicate atom serial number found: 8969  
Duplicate atom serial number found: 8970  
20 messages similar to the above omitted  
  
Chain information for V15_holo-coot-1.pdb #12  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V17_holo-
> coot-3.pdb

Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V17_holo-
coot-3.pdb  
---  
warnings | Duplicate atom serial number found: 8965  
Duplicate atom serial number found: 8966  
Duplicate atom serial number found: 8967  
Duplicate atom serial number found: 8968  
Duplicate atom serial number found: 8969  
22 messages similar to the above omitted  
  
Chain information for V17_holo-coot-3.pdb #13  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V18_holo-
> coot-1.pdb

Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V18_holo-
coot-1.pdb  
---  
warnings | Duplicate atom serial number found: 8965  
Duplicate atom serial number found: 8966  
Duplicate atom serial number found: 8967  
Duplicate atom serial number found: 8968  
Duplicate atom serial number found: 8969  
24 messages similar to the above omitted  
  
Chain information for V18_holo-coot-1.pdb #14  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V19_holo-
> coot-6.pdb

Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V19_holo-
coot-6.pdb  
---  
warnings | Duplicate atom serial number found: 8965  
Duplicate atom serial number found: 8966  
Duplicate atom serial number found: 8967  
Duplicate atom serial number found: 8968  
Duplicate atom serial number found: 8969  
26 messages similar to the above omitted  
  
Chain information for V19_holo-coot-6.pdb #15  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V21_holo-
> coot-2.pdb

Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V21_holo-
coot-2.pdb  
---  
warnings | Duplicate atom serial number found: 8964  
Duplicate atom serial number found: 8965  
Duplicate atom serial number found: 8966  
Duplicate atom serial number found: 8967  
Duplicate atom serial number found: 8968  
23 messages similar to the above omitted  
  
Chain information for V21_holo-coot-2.pdb #16  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V23_holo-
> coot-2.pdb

Chain information for V23_holo-coot-2.pdb #17  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V25_holo-
> coot-2.pdb

Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V25_holo-
coot-2.pdb  
---  
warnings | Duplicate atom serial number found: 8964  
Duplicate atom serial number found: 8965  
Duplicate atom serial number found: 8966  
Duplicate atom serial number found: 8967  
Duplicate atom serial number found: 8968  
30 messages similar to the above omitted  
  
Chain information for V25_holo-coot-2.pdb #18  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Computing secondary structure  
[Repeated 2 time(s)]

> select #1/A:59, 60, 78, 79,49, 51, 394, 395,49, 394, 395,272, 273, 274,
> 275,113, 114, 136,277, 278, 329, 330, 331,274, 275, 276, 277, 301,256, 257,
> 258,100, 101, 102, 103, 104,100, 101, 102, 103,285, 298, 299,291, 292, 293,
> 294,299, 300, 301, 302,49, 50, 51, 388, 389, 390,59, 60, 78, 79,80, 81

983 atoms, 1091 bonds, 45 residues, 1 model selected  

> hide #2-18 target m

> select #1/A:59, 60, 78, 79,49, 51, 394, 395,49, 394, 395,272, 273, 274,
> 275,113, 114, 136,277, 278, 329, 330, 331,274, 275, 276, 277, 301,256, 257,
> 258,100, 101, 102, 103, 104,100, 101, 102, 103,285, 298, 299,291, 292, 293,
> 294,299, 300, 301, 302,49, 50, 51, 388, 389, 390,59, 60, 78, 79,80, 81

983 atoms, 1091 bonds, 45 residues, 1 model selected  

> select #8/A:100, 101, 102, 103,256, 257, 258,261, 271, 272, 273,26, 27, 28,
> 41,275, 276, 332, 333,275, 276, 333,49, 50, 51, 388, 389, 390,48, 50, 386,
> 387, 399,385, 386, 387,291, 292, 293, 294,277, 278, 329, 330, 331,275, 276,
> 333,113, 114, 136,15, 16, 17,25, 26, 274, 332,25, 26, 332,26, 274, 332,272,
> 273, 274,272, 273, 274, 275,273, 333,337, 338, 388,337, 388,382, 383,
> 384,49, 389, 390, 392, 393,49, 394, 395,49, 51, 394, 395,56, 57, 254,59, 60,
> 78, 79,61, 81, 250,80, 81

1459 atoms, 1618 bonds, 67 residues, 1 model selected  

> show #8 models

> hide #1 models

> select
> #1/A:15,21-29,39-67,69-84,96-101,105-112,249-261,272-293,295-312,327-340,386-400

3255 atoms, 3639 bonds, 151 residues, 1 model selected  

> hide #8 models

> show #1 models

> show #2-18 target m

> ui tool show Matchmaker

> matchmaker #2-18 to #1 & sel matrix Nucleic

Computing secondary structure  
[Repeated 17 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V3_holo-coot-2.pdb, chain A
(#2), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.380 angstroms; (across all 151 pairs:
0.413)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V4_holo-coot-3.pdb, chain A
(#3), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.322 angstroms; (across all 151 pairs:
0.322)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V5_holo-coot-1.pdb, chain A
(#4), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.445 angstroms; (across all 151 pairs:
0.445)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V6_holo-coot-1.pdb, chain A
(#5), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.365 angstroms; (across all 151 pairs:
0.365)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V7_holo-coot-2.pdb, chain A
(#6), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.323 angstroms; (across all 151 pairs:
0.323)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V9_holo-coot-0.pdb, chain A
(#7), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.325 angstroms; (across all 151 pairs:
0.325)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V10_holo-coot-1.pdb, chain A
(#8), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.364 angstroms; (across all 151 pairs:
0.364)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V11_holo-coot-1.pdb, chain A
(#9), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.374 angstroms; (across all 151 pairs:
0.374)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V12_holo-coot-3.pdb, chain A
(#10), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.367 angstroms; (across all 151 pairs:
0.367)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V14_holo-coot-1.pdb, chain A
(#11), sequence alignment score = 604  
RMSD between 149 pruned atom pairs is 0.402 angstroms; (across all 151 pairs:
0.464)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V15_holo-coot-1.pdb, chain A
(#12), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.359 angstroms; (across all 151 pairs:
0.359)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V17_holo-coot-3.pdb, chain A
(#13), sequence alignment score = 604  
RMSD between 149 pruned atom pairs is 0.351 angstroms; (across all 151 pairs:
0.441)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V18_holo-coot-1.pdb, chain A
(#14), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.367 angstroms; (across all 151 pairs:
0.367)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V19_holo-coot-6.pdb, chain A
(#15), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.488 angstroms; (across all 151 pairs:
0.488)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V21_holo-coot-2.pdb, chain A
(#16), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.445 angstroms; (across all 151 pairs:
0.445)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V23_holo-coot-2.pdb, chain A
(#17), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.368 angstroms; (across all 151 pairs:
0.368)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V25_holo-coot-2.pdb, chain A
(#18), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.430 angstroms; (across all 151 pairs:
0.430)  
  

> select

178904 atoms, 198000 bonds, 10136 residues, 18 models selected  

> hide sel target a

> select #1/C

31 atoms, 31 residues, 1 model selected  

> select #1-18/C

542 atoms, 542 residues, 18 models selected  

> show sel target ab

> style sel sphere

Changed 542 atom styles  

> hide #2-18 target m

> hide #1 models

> show #1 models

> show #2 models

> hide #1 models

> show #1 models

> hide #1 models

> show #3 models

> hide #3 models

> show #4 models

> hide #4 models

> show #5 models

> hide #5 models

> show #6 models

> hide #6 models

> show #7 models

> hide #7 models

> show #8 models

> hide #8 models

> show #9 models

> hide #9 models

> show #10 models

> hide #10 models

> show #11 models

> show #12 models

> show #13 models

> hide #13 models

> show #13 models

> hide #13 models

> show #14 models

> hide #14 models

> show #15 models

> show #16 models

> show #17 models

> hide #17 models

> show #18 models

> select #1-18/C/7

542 atoms, 542 residues, 18 models selected  

> select #1-18/C:7

18 atoms, 18 residues, 18 models selected  

> select #1-18/C:4

18 atoms, 18 residues, 18 models selected  

> select #1-18/C:24

12 atoms, 12 residues, 12 models selected  

> select clear

> hide #2 models

> hide #11 models

> hide #12 models

> hide #15 models

> hide #16 models

> hide #18 models

> show #1 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #3 models

> show #2 models

> show #4 models

> show #5 models

> hide #5 models

> show #5 models

> show #6 models

> show #7 models

> show #8 models

> show #9 models

> show #10 models

> show #11 models

> show #12 models

> show #13 models

> show #14 models

> show #15 models

> show #16 models

> show #17 models

> show #18 models

> set bgColor white

> select #1-18/A

161316 atoms, 180684 bonds, 7506 residues, 18 models selected  

> ui tool show "Color Actions"

> color sel light slate gray

> select #1-18/B

17046 atoms, 17316 bonds, 2088 residues, 18 models selected  

> ui tool show "Color Actions"

> color sel plum

> surface sel

> surface hidePatches (#!1-18 & sel)

> select #1/B

947 atoms, 962 bonds, 116 residues, 1 model selected  

> surface (#!1 & sel)

> surface hidePatches (#!1 & sel)

> surface (#!1 & sel)

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for V2_holo-coot-2.pdb_B SES surface #1.1: minimum, -9.82,
mean 5.09, maximum 22.28  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> surface hidePatches (#!1 & sel)

> select #1-18/C:1

7 atoms, 7 residues, 7 models selected  

> select #1-18/A:50,389,390

1188 atoms, 1314 bonds, 54 residues, 18 models selected  

> cartoon hide sel

> show sel target ab

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> hide sel target a

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab

> show (sel-residues & sidechain) target ab

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> hide sel target a

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> nucleotides sel atoms

> style nucleic & sel stick

Changed 1188 atom styles  

> select #1-18/A:7

360 atoms, 378 bonds, 18 residues, 18 models selected  

> select #1-18/A:50,389,390

1188 atoms, 1314 bonds, 54 residues, 18 models selected  

> color sel red

> select #6/A:392

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #15/A:393

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #3/C:68@MG

1 atom, 1 residue, 1 model selected  

> select up

35 atoms, 35 residues, 1 model selected  

> select #1-18/C:7

18 atoms, 18 residues, 18 models selected  

> ui tool show "Selection Inspector"

> size sel atomRadius 0.7

Changed 18 atom radii  

> color sel red

> select #1-18/A:50,389,390

1188 atoms, 1314 bonds, 54 residues, 18 models selected  

> ui tool show "Color Actions"

> color sel brown

> color sel coral

> color sel orange

> color sel coral

> color sel tomato

> color sel coral

> select #14/C:80@MG

1 atom, 1 residue, 1 model selected  

> select add #13/C:7@MG

2 atoms, 2 residues, 2 models selected  

> ui tool show Distances

> distance #14/C:80@MG #13/C:7@MG

Distance between V18_holo-coot-1.pdb #14/C MG 80 MG and V17_holo-coot-3.pdb
#13/C MG 7 MG: 14.313Å  

> select #10/C:80@MG

1 atom, 1 residue, 1 model selected  

> select add #12/C:7@MG

2 atoms, 2 residues, 2 models selected  

> distance #10/C:80@MG #12/C:7@MG

Distance between V12_holo-coot-3.pdb #10/C MG 80 MG and V15_holo-coot-1.pdb
#12/C MG 7 MG: 12.866Å  

> hide #!1-18 target m

> show #!1 models

> show #!2 models

> show #!3 models

> show #!4 models

> show #!5 models

> show #!6 models

> hide #!6 models

> show #!6 models

> show #!7 models

> show #!8 models

> show #!9 models

> show #!10 models

> hide #!10 models

> show #!10 models

> show #!11 models

> show #!12 models

> hide #!12 models

> show #!12 models

> show #!13 models

> show #!14 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> select #6/C:24@MG

1 atom, 1 residue, 1 model selected  

> select add #6/C:75@MG

2 atoms, 2 residues, 1 model selected  

> distance #6/C:24@MG #6/C:75@MG

Distance between V7_holo-coot-2.pdb #6/C MG 24 MG and MG 75 MG: 6.929Å  

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select add #6/C:24@MG

2 atoms, 2 residues, 2 models selected  

> distance #10/C:84@MG #6/C:24@MG

Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and V7_holo-coot-2.pdb
#6/C MG 24 MG: 3.368Å  

> select #6/C:24@MG

1 atom, 1 residue, 1 model selected  

> select add #5/C:7@MG

2 atoms, 2 residues, 2 models selected  

> distance #6/C:24@MG #5/C:7@MG

Distance between V7_holo-coot-2.pdb #6/C MG 24 MG and V6_holo-coot-1.pdb #5/C
MG 7 MG: 7.527Å  

> select #9/C:4@MG

1 atom, 1 residue, 1 model selected  

> select add #12/C:7@MG

2 atoms, 2 residues, 2 models selected  

> distance #9/C:4@MG #12/C:7@MG

Distance between V11_holo-coot-1.pdb #9/C MG 4 MG and V15_holo-coot-1.pdb
#12/C MG 7 MG: 9.036Å  

> ~distance #6/C:24@MG #6/C:75@MG

> ~distance #9/C:4@MG #12/C:7@MG

> ~distance #14/C:80@MG #13/C:7@MG

> ~distance #10/C:84@MG #6/C:24@MG

> ~distance #6/C:24@MG #5/C:7@MG

> ~distance #10/C:80@MG #12/C:7@MG

> select #1-18/A:50,389,390

1188 atoms, 1314 bonds, 54 residues, 18 models selected  

> ui tool show "Color Actions"

> color sel tomato

> color sel chocolate

> color sel fire brick

> color sel coral

> color sel goldenrod

> color (#!1-14 & sel) #ff2600ff

> color sel sienna

> color sel cyan

> color sel medium blue

> color sel cornflower blue

> select #1-18/C:7

18 atoms, 18 residues, 18 models selected  

> color (#!1-14 & sel) blue

> color sel red

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/pdb_models_YTZ/holoES-
> pretRNA-5mM-Ca/Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb

Chain information for Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb
#19  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
E | No description available  
  
Computing secondary structure  

> select up

542 atoms, 542 residues, 18 models selected  

> select up

178904 atoms, 198000 bonds, 10136 residues, 18 models selected  

> select
> #1/A:15,21-29,39-67,69-84,96-101,105-112,249-261,272-293,295-312,327-340,386-400

3255 atoms, 3639 bonds, 151 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #19 to #1 & sel matrix Nucleic

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with Ternary_pretRNA_5mM_Ca-
coot-7_real_space_refined_018.pdb, chain A (#19), sequence alignment score =
604  
RMSD between 150 pruned atom pairs is 0.728 angstroms; (across all 151 pairs:
0.766)  
  

> select #19

12016 atoms, 13315 bonds, 661 residues, 1 model selected  

> hide sel target a

> select #19/C

1889 atoms, 2107 bonds, 89 residues, 1 model selected  

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> color sel yellow

> select #19/D

30 atoms, 30 residues, 1 model selected  

> show sel target ab

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select clear

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select add #11/A:390@OP2

2 atoms, 2 residues, 2 models selected  

> distance #10/C:84@MG #11/A:390@OP2

Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and V14_holo-coot-1.pdb
#11/A A 390 OP2: 3.278Å  

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select #19/D:5@CA

1 atom, 1 residue, 1 model selected  

> select add #10/C:84@MG

2 atoms, 2 residues, 2 models selected  

> distance #19/D:5@CA #10/C:84@MG

Distance between Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb
#19/D CA 5 CA and V12_holo-coot-3.pdb #10/C MG 84 MG: 6.302Å  

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select add #19/D:30@CA

2 atoms, 2 residues, 2 models selected  

> distance #10/C:84@MG #19/D:30@CA

Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and
Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/D CA 30 CA:
7.802Å  

> hide #19 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> select #13/C:24@MG

1 atom, 1 residue, 1 model selected  

> select #9/C:24@MG

1 atom, 1 residue, 1 model selected  

> select add #10/C:84@MG

2 atoms, 2 residues, 2 models selected  

> distance #9/C:24@MG #10/C:84@MG

Distance between V11_holo-coot-1.pdb #9/C MG 24 MG and V12_holo-coot-3.pdb
#10/C MG 84 MG: 3.570Å  

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> hide #!1-14 target m

> show #!12 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> hide #!12 models

> show #!10 models

> show #19 models

> select #19/C:0

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #19/C:1

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #19/C:0

43 atoms, 46 bonds, 2 residues, 1 model selected  

> hide #19 models

> show #!1-18 target m

> select #10/C:80@MG

1 atom, 1 residue, 1 model selected  

> select clear

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> select #1-18/

Expected an objects specifier or a keyword  

> select #1-18

178904 atoms, 198000 bonds, 2 pseudobonds, 10136 residues, 19 models selected  

> select #1-18/C

542 atoms, 1 pseudobond, 542 residues, 19 models selected  

> ui tool show "Color Actions"

> color sel forest green

> select #1-18/C:7

18 atoms, 18 residues, 18 models selected  

> ui tool show "Color Actions"

> color sel dark red

[Repeated 1 time(s)]

> color sel maroon

> color sel dark red

> ui tool show "Selection Inspector"

> ~distance #10/C:84@MG #11/A:390@OP2

> ~distance #19/D:5@CA #10/C:84@MG

> ~distance #9/C:24@MG #10/C:84@MG

> ~distance #10/C:84@MG #19/D:30@CA

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select add #17/C:87@MG

2 atoms, 2 residues, 2 models selected  

> select #1-18/C

542 atoms, 542 residues, 18 models selected  

> ui tool show "Selection Inspector"

> size sel atomRadius 0.7

Changed 542 atom radii  

> select #13/C:22@MG

1 atom, 1 residue, 1 model selected  

> select #1-18/C:9

16 atoms, 16 residues, 16 models selected  

> color sel blue

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> select #18/C:62@MG

1 atom, 1 residue, 1 model selected  

> select add #19/A:279

21 atoms, 21 bonds, 2 residues, 2 models selected  

> select #19/C:3

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #1-18/C:12

17 atoms, 17 residues, 17 models selected  

> color sel blue

> select #18/C:62@MG

1 atom, 1 residue, 1 model selected  

> select add #19/C:3

24 atoms, 25 bonds, 2 residues, 2 models selected  

> select #19/C:3

23 atoms, 25 bonds, 1 residue, 1 model selected  

> show sel target ab

> cartoon hide sel

> select #19/C:3@C5'

1 atom, 1 residue, 1 model selected  

> select add #18/C:62@MG

2 atoms, 2 residues, 2 models selected  

> distance #19/C:3@C5' #18/C:62@MG

Distance between Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb
#19/C G 3 C5' and V25_holo-coot-2.pdb #18/C MG 62 MG: 7.071Å  

> view matrix models
> #18,0.99985,0.00571,-0.016139,1.607,-0.0060653,0.99974,-0.02205,5.6923,0.016009,0.022145,0.99963,-5.4963,#19,-0.96809,0.078949,-0.23783,410.8,0.24041,0.024802,-0.97035,327.08,-0.070709,-0.99657,-0.042991,409.72

> view matrix models
> #18,0.98188,-0.025202,-0.18781,39.726,0.0089682,0.99619,-0.086791,14.256,0.18928,0.083534,0.97836,-47.209,#19,-0.9475,0.24905,-0.20055,362.29,0.2289,0.090348,-0.96925,314.7,-0.22327,-0.96427,-0.14261,451.61

> view matrix models
> #18,0.98928,0.0045084,-0.14599,25.485,-0.014636,0.99755,-0.068373,15.45,0.14533,0.069777,0.98692,-37.485,#19,-0.95027,0.20788,-0.2319,377.78,0.25102,0.070488,-0.96541,313.97,-0.18434,-0.97561,-0.11916,442

> view matrix models
> #18,0.98454,-0.024891,-0.17338,36.644,0.017984,0.99899,-0.041293,4.3816,0.17423,0.037537,0.98399,-35.839,#19,-0.95088,0.23482,-0.20172,366.2,0.21806,0.045516,-0.97487,327.75,-0.21974,-0.97097,-0.094484,443.7

> view matrix models
> #18,0.98484,0.054997,-0.16452,19.343,-0.062648,0.99717,-0.041676,20.275,0.16176,0.051351,0.98549,-36.422,#19,-0.93307,0.22625,-0.27964,379.17,0.29591,0.040826,-0.95434,309.51,-0.2045,-0.97321,-0.10504,443.16

> matchmaker #!2-11 to #1 & sel matrix Nucleic

No 'to' model specified  

> select
> #1/A:15,21-29,39-67,69-84,96-101,105-112,249-261,272-293,295-312,327-340,386-400

3255 atoms, 3639 bonds, 151 residues, 1 model selected  

> matchmaker #!2-11 to #1 & sel matrix Nucleic

Computing secondary structure  
[Repeated 10 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V3_holo-coot-2.pdb, chain A
(#2), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.380 angstroms; (across all 151 pairs:
0.413)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V4_holo-coot-3.pdb, chain A
(#3), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.322 angstroms; (across all 151 pairs:
0.322)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V5_holo-coot-1.pdb, chain A
(#4), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.445 angstroms; (across all 151 pairs:
0.445)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V6_holo-coot-1.pdb, chain A
(#5), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.365 angstroms; (across all 151 pairs:
0.365)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V7_holo-coot-2.pdb, chain A
(#6), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.323 angstroms; (across all 151 pairs:
0.323)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V9_holo-coot-0.pdb, chain A
(#7), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.325 angstroms; (across all 151 pairs:
0.325)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V10_holo-coot-1.pdb, chain A
(#8), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.364 angstroms; (across all 151 pairs:
0.364)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V11_holo-coot-1.pdb, chain A
(#9), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.374 angstroms; (across all 151 pairs:
0.374)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V12_holo-coot-3.pdb, chain A
(#10), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.367 angstroms; (across all 151 pairs:
0.367)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V14_holo-coot-1.pdb, chain A
(#11), sequence alignment score = 604  
RMSD between 149 pruned atom pairs is 0.402 angstroms; (across all 151 pairs:
0.464)  
  

> matchmaker #19#!2-18 to #1 & sel matrix Nucleic

Computing secondary structure  
[Repeated 18 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with Ternary_pretRNA_5mM_Ca-
coot-7_real_space_refined_018.pdb, chain A (#19), sequence alignment score =
604  
RMSD between 150 pruned atom pairs is 0.728 angstroms; (across all 151 pairs:
0.766)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V3_holo-coot-2.pdb, chain A
(#2), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.380 angstroms; (across all 151 pairs:
0.413)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V4_holo-coot-3.pdb, chain A
(#3), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.322 angstroms; (across all 151 pairs:
0.322)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V5_holo-coot-1.pdb, chain A
(#4), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.445 angstroms; (across all 151 pairs:
0.445)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V6_holo-coot-1.pdb, chain A
(#5), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.365 angstroms; (across all 151 pairs:
0.365)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V7_holo-coot-2.pdb, chain A
(#6), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.323 angstroms; (across all 151 pairs:
0.323)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V9_holo-coot-0.pdb, chain A
(#7), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.325 angstroms; (across all 151 pairs:
0.325)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V10_holo-coot-1.pdb, chain A
(#8), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.364 angstroms; (across all 151 pairs:
0.364)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V11_holo-coot-1.pdb, chain A
(#9), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.374 angstroms; (across all 151 pairs:
0.374)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V12_holo-coot-3.pdb, chain A
(#10), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.367 angstroms; (across all 151 pairs:
0.367)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V14_holo-coot-1.pdb, chain A
(#11), sequence alignment score = 604  
RMSD between 149 pruned atom pairs is 0.402 angstroms; (across all 151 pairs:
0.464)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V15_holo-coot-1.pdb, chain A
(#12), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.359 angstroms; (across all 151 pairs:
0.359)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V17_holo-coot-3.pdb, chain A
(#13), sequence alignment score = 604  
RMSD between 149 pruned atom pairs is 0.351 angstroms; (across all 151 pairs:
0.441)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V18_holo-coot-1.pdb, chain A
(#14), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.367 angstroms; (across all 151 pairs:
0.367)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V19_holo-coot-6.pdb, chain A
(#15), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.488 angstroms; (across all 151 pairs:
0.488)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V21_holo-coot-2.pdb, chain A
(#16), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.445 angstroms; (across all 151 pairs:
0.445)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V23_holo-coot-2.pdb, chain A
(#17), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.368 angstroms; (across all 151 pairs:
0.368)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V25_holo-coot-2.pdb, chain A
(#18), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.430 angstroms; (across all 151 pairs:
0.430)  
  

> ui mousemode right select

> select clear

Drag select of 6 residues  

> select clear

> hide #!1-18 target m

> show #!1 models

> hide #!1 models

> show #!1 models

> show #!1-18 target m

Drag select of 17 residues  

> select clear

> select #1-18/C:10

13 atoms, 13 residues, 13 models selected  
Drag select of 6 residues  

> select #19/C:0

20 atoms, 21 bonds, 1 residue, 1 model selected  

> hide #19 models

> select #14/C:80@MG

1 atom, 1 residue, 1 model selected  

> select subtract #14/C:80@MG

Nothing selected  

> select add #5/C:24@MG

1 atom, 1 residue, 1 model selected  

> select add #14/C:80@MG

2 atoms, 2 residues, 2 models selected  

> select #7/A:278

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #14/C:80@MG

1 atom, 1 residue, 1 model selected  

> select #1-18/A:50,389,390

1188 atoms, 1314 bonds, 54 residues, 18 models selected  

> select #1-18/A:49,50,51,389,390

1998 atoms, 2232 bonds, 90 residues, 18 models selected  

> select #7/A:391

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1-18/A:49,50,51,389,390,391

2358 atoms, 2628 bonds, 108 residues, 18 models selected  

> select #1-18/A:49,50,51,52,388,389,390,391

3132 atoms, 3492 bonds, 144 residues, 18 models selected  

> show #19 models

> hide #19 models

> view sel

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select add #17/C:87@MG

2 atoms, 2 residues, 2 models selected  

> select add #1/C:4@MG

3 atoms, 3 residues, 3 models selected  

> select add #13/C:24@MG

4 atoms, 4 residues, 4 models selected  

> select add #11/A:390@OP2

5 atoms, 5 residues, 5 models selected  

> select add #12/C:7@MG

6 atoms, 6 residues, 6 models selected  

> select add #4/A:50@OP1

7 atoms, 7 residues, 7 models selected  

> view sel

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> select #7/A:390@O3'

1 atom, 1 residue, 1 model selected  

> select #7/A:390@O3'

1 atom, 1 residue, 1 model selected  

> select add #4/A:390@O2'

2 atoms, 2 residues, 2 models selected  

> select add #11/A:390@OP2

3 atoms, 3 residues, 3 models selected  

> select add #12/C:7@MG

4 atoms, 4 residues, 4 models selected  

> select add #13/C:7@MG

5 atoms, 5 residues, 5 models selected  

> select add #11/A:389@O5'

6 atoms, 6 residues, 5 models selected  

> select add #6/A:389@OP2

7 atoms, 7 residues, 6 models selected  

> select add #11/A:50@OP2

8 atoms, 8 residues, 6 models selected  

> select add #4/A:50@OP1

9 atoms, 9 residues, 6 models selected  

> select add #2/A:51

32 atoms, 25 bonds, 10 residues, 7 models selected  

> select add #17/A:49

54 atoms, 49 bonds, 11 residues, 8 models selected  

> select add #8/A:50@O2'

55 atoms, 49 bonds, 12 residues, 9 models selected  

> select add #11/A:50@O3'

56 atoms, 49 bonds, 12 residues, 9 models selected  

> select add #13/C:24@MG

57 atoms, 49 bonds, 13 residues, 9 models selected  

> select add #10/C:84@MG

58 atoms, 49 bonds, 14 residues, 10 models selected  

> select add #17/C:87@MG

59 atoms, 49 bonds, 15 residues, 10 models selected  

> select add #9/C:4@MG

60 atoms, 49 bonds, 16 residues, 11 models selected  

> view sel

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> select #13/C:7@MG

1 atom, 1 residue, 1 model selected  

> select add #17/C:82@MG

2 atoms, 2 residues, 2 models selected  

> distance #13/C:7@MG #17/C:82@MG

Distance between V17_holo-coot-3.pdb #13/C MG 7 MG and V23_holo-coot-2.pdb
#17/C MG 82 MG: 13.090Å  

> distance #13/C:7@MG #17/C:82@MG

Distance already exists; modify distance properties with 'distance style'  

> ~distance #19/C:3@C5' #18/C:62@MG

> ~distance #13/C:7@MG #17/C:82@MG

> select clear

> select #4/C:24@MG

1 atom, 1 residue, 1 model selected  

> select add #7/C:24@MG

2 atoms, 2 residues, 2 models selected  

> select add #18/C:24@MG

3 atoms, 3 residues, 3 models selected  

> select add #9/C:24@MG

4 atoms, 4 residues, 4 models selected  

> select add #3/C:24@MG

5 atoms, 5 residues, 5 models selected  

> select add #13/C:24@MG

6 atoms, 6 residues, 6 models selected  

> select add #6/C:24@MG

7 atoms, 7 residues, 7 models selected  

> select add #10/C:84@MG

8 atoms, 8 residues, 8 models selected  

> select add #17/C:87@MG

9 atoms, 9 residues, 9 models selected  

> select add #4/C:4@MG

10 atoms, 10 residues, 9 models selected  

> select add #8/C:4@MG

11 atoms, 11 residues, 10 models selected  

> select add #1/C:4@MG

12 atoms, 12 residues, 11 models selected  

> select add #9/C:4@MG

13 atoms, 13 residues, 11 models selected  

> select add #6/A:50@OP2

14 atoms, 14 residues, 11 models selected  

> select add #11/A:50@P

15 atoms, 15 residues, 12 models selected  

> select add #5/A:50@OP1

16 atoms, 16 residues, 13 models selected  

> select add #12/C:7@MG

17 atoms, 17 residues, 14 models selected  

> select add #13/C:7@MG

18 atoms, 18 residues, 14 models selected  

> select add #11/A:390@OP1

19 atoms, 19 residues, 14 models selected  

> select add #15/A:390@OP1

20 atoms, 20 residues, 15 models selected  

> select add #5/A:389@O2'

21 atoms, 21 residues, 15 models selected  

> select add #7/A:390@O2'

22 atoms, 22 residues, 15 models selected  

> select add #7/A:390@C5'

23 atoms, 22 residues, 15 models selected  

> select add #6/A:390@O5'

24 atoms, 23 residues, 15 models selected  

> select add #17/A:389@O5'

25 atoms, 24 residues, 15 models selected  

> select add #11/A:389@C4'

26 atoms, 25 residues, 15 models selected  

> select add #11/A:389@OP2

27 atoms, 25 residues, 15 models selected  

> select add #17/A:388

50 atoms, 25 bonds, 26 residues, 15 models selected  

> select add #4/A:51

73 atoms, 50 bonds, 27 residues, 15 models selected  

> select add #2/A:50@C5'

74 atoms, 50 bonds, 28 residues, 16 models selected  

> select add #4/A:50@O5'

75 atoms, 50 bonds, 29 residues, 16 models selected  

> select add #14/A:52

95 atoms, 71 bonds, 30 residues, 17 models selected  

> select add #17/A:49

117 atoms, 95 bonds, 31 residues, 17 models selected  

> view sel

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> select #3/C:68@MG

1 atom, 1 residue, 1 model selected  

> select add #13/C:7@MG

2 atoms, 2 residues, 2 models selected  

> show #19 models

> select #3/C:68@MG

1 atom, 1 residue, 1 model selected  

> select add #19/C:-1

21 atoms, 21 bonds, 2 residues, 2 models selected  
Exactly two atoms must be selected!  

> select #3/C:68@MG

1 atom, 1 residue, 1 model selected  

> hide sel target a

> hide #!18 models

> show #!18 models

> hide #19 models

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select #17/C:87@MG

1 atom, 1 residue, 1 model selected  

> show #19 models

> hide #19 models

> select clear

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select add #17/C:87@MG

2 atoms, 2 residues, 2 models selected  

> select add #13/C:7@MG

3 atoms, 3 residues, 3 models selected  

> view sel

> select add #13/C:24@MG

4 atoms, 4 residues, 3 models selected  

> select add #18/C:62@MG

5 atoms, 5 residues, 4 models selected  

> view sel

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> hide #19 models

> show #19 models

> hide #19 models

> select #6/A:50@OP2

1 atom, 1 residue, 1 model selected  

> select add #13/C:7@MG

2 atoms, 2 residues, 2 models selected  

> select add #11/A:390@OP1

3 atoms, 3 residues, 3 models selected  

> select add #10/C:84@MG

4 atoms, 4 residues, 4 models selected  

> select add #18/C:24@MG

5 atoms, 5 residues, 5 models selected  

> select add #9/C:4@MG

6 atoms, 6 residues, 6 models selected  

> select add #4/C:4@MG

7 atoms, 7 residues, 7 models selected  

> select add #1/C:4@MG

8 atoms, 8 residues, 8 models selected  

> select add #17/C:87@MG

9 atoms, 9 residues, 9 models selected  

> select add #13/C:24@MG

10 atoms, 10 residues, 9 models selected  

> select add #6/C:24@MG

11 atoms, 11 residues, 9 models selected  

> select add #12/C:7@MG

12 atoms, 12 residues, 10 models selected  

> select add #3/C:7@MG

13 atoms, 13 residues, 11 models selected  

> select add #5/A:50@OP1

14 atoms, 14 residues, 12 models selected  

> select add #17/A:389@OP2

15 atoms, 15 residues, 12 models selected  

> select add #6/A:389@OP2

16 atoms, 16 residues, 12 models selected  

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17 atoms, 17 residues, 13 models selected  

> select add #9/A:390@OP2

18 atoms, 18 residues, 13 models selected  

> view sel

> select #17/C:87@MG

1 atom, 1 residue, 1 model selected  

> view sel

> select #1-18/A:49,50,51,52,388,389,390,391

3132 atoms, 3492 bonds, 144 residues, 18 models selected  

> view sel

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select add #3/C:24@MG

2 atoms, 2 residues, 2 models selected  

> select add #13/C:24@MG

3 atoms, 3 residues, 3 models selected  

> select add #18/C:24@MG

4 atoms, 4 residues, 4 models selected  

> select add #9/A:390@OP2

5 atoms, 5 residues, 5 models selected  

> select add #13/C:7@MG

6 atoms, 6 residues, 5 models selected  

> select add #17/C:87@MG

7 atoms, 7 residues, 6 models selected  

> select add #1/C:4@MG

8 atoms, 8 residues, 7 models selected  

> select #1-18/A:49,50,51,52,388,389,390,391

3132 atoms, 3492 bonds, 144 residues, 18 models selected  

> select add #10/C:84@MG

3133 atoms, 3492 bonds, 145 residues, 18 models selected  

> select add #17/C:87@MG

3134 atoms, 3492 bonds, 146 residues, 18 models selected  

> select add #3/C:24@MG

3135 atoms, 3492 bonds, 147 residues, 18 models selected  

> select add #6/C:24@MG

3136 atoms, 3492 bonds, 148 residues, 18 models selected  

> select add #9/C:24@MG

3137 atoms, 3492 bonds, 149 residues, 18 models selected  

> select add #18/C:24@MG

3138 atoms, 3492 bonds, 150 residues, 18 models selected  

> select add #1/C:4@MG

3139 atoms, 3492 bonds, 151 residues, 18 models selected  

> select add #4/C:4@MG

3140 atoms, 3492 bonds, 152 residues, 18 models selected  

> select add #9/C:4@MG

3141 atoms, 3492 bonds, 153 residues, 18 models selected  

> select add #18/C:4@MG

3142 atoms, 3492 bonds, 154 residues, 18 models selected  

> select add #12/C:7@MG

3143 atoms, 3492 bonds, 155 residues, 18 models selected  

> select add #13/C:7@MG

3144 atoms, 3492 bonds, 156 residues, 18 models selected  

> select add #3/C:7@MG

3145 atoms, 3492 bonds, 157 residues, 18 models selected  

> view sel

> show #19 models

> hide #19 models

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> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select clear

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select add #17/C:87@MG

2 atoms, 2 residues, 2 models selected  

> color sel magenta

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No map chosen to save  

> save
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/apo_holo_analysis/ions/ions_holo_new_core_aa_models.cxs

> show #19 models

> select #19/C:4

23 atoms, 25 bonds, 1 residue, 1 model selected  

> hide sel target a

> cartoon hide sel

> select #19/C:2

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #19/C:1

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select add #19/C:0

63 atoms, 67 bonds, 3 residues, 1 model selected  

> select #19/C:2

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #19/C:1

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select add #19/C:0

63 atoms, 67 bonds, 3 residues, 1 model selected  

> show sel target ab

> cartoon hide sel

> nucleotides sel atoms

> style nucleic & sel stick

Changed 63 atom styles  

> select #1/A:49,50,51,52,388,389,390,391

174 atoms, 194 bonds, 8 residues, 1 model selected  

> matchmaker #19 to #1 & sel matrix Nucleic

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with Ternary_pretRNA_5mM_Ca-
coot-7_real_space_refined_018.pdb, chain A (#19), sequence alignment score =
32  
RMSD between 8 pruned atom pairs is 0.305 angstroms; (across all 8 pairs:
0.305)  
  

> select #19/A

8962 atoms, 10038 bonds, 417 residues, 1 model selected  

> hide sel target a

> cartoon hide sel

> select #19/C:2

20 atoms, 21 bonds, 1 residue, 1 model selected  

> hide sel target a

> select #19/C

1889 atoms, 2107 bonds, 89 residues, 1 model selected  

> nucleotides sel tube/slab shape ellipsoid

> nucleotides sel atoms

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> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> select #19/C:2-40

835 atoms, 934 bonds, 39 residues, 1 model selected  

> hide sel target a

> select #19/C

1889 atoms, 2107 bonds, 89 residues, 1 model selected  

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[Repeated 2 time(s)]

> color sel #2e2e2eff

> color sel #303030ff

> color sel #343434ff

> color sel #393939ff

> color sel #3d3d3dff

> color sel #434343ff

> color sel #4a4a4aff

> color sel #4d4d4dff

> color sel #515151ff

> color sel #525252ff

> color sel #535353ff

> color sel #545454ff

> color sel #555555ff

> color sel #565656ff

> color sel #575757ff

> color sel #585858ff

[Repeated 1 time(s)]

> color sel #595959ff

> color sel #5a5a5aff

> color sel #5c5c5cff

> color sel #5e5e5eff

> color sel #5f5f5fff

> color sel #606060ff

> color sel #616161ff

[Repeated 1 time(s)]

> color sel #626262ff

[Repeated 3 time(s)]

> color sel #636363ff

[Repeated 1 time(s)]

> color sel #646464ff

[Repeated 2 time(s)]

> color sel #656565ff

[Repeated 1 time(s)]

> color sel #666666ff

[Repeated 2 time(s)]

> color sel #676767ff

[Repeated 1 time(s)]

> color sel #686868ff

[Repeated 1 time(s)]

> color sel #696969ff

> color sel #6a6a6aff

> color sel #6b6b6bff

[Repeated 1 time(s)]

> color sel #6a6a6aff

> color sel #686868ff

> color sel #676767ff

> color sel #666666ff

> color sel #646464ff

[Repeated 1 time(s)]

> color sel #626262ff

> color sel #616161ff

> color sel #5f5f5fff

[Repeated 1 time(s)]

> color sel #5e5e5eff

> color sel #5d5d5dff

[Repeated 1 time(s)]

> color sel #5c5c5cff

[Repeated 1 time(s)]

> color sel #5b5b5bff

[Repeated 2 time(s)]

> color sel #5a5a5aff

[Repeated 1 time(s)]

> color sel #595959ff

[Repeated 2 time(s)]

> color sel #585858ff

[Repeated 2 time(s)]

> color sel #575757ff

[Repeated 1 time(s)]

> color sel #565656ff

[Repeated 1 time(s)]

> color sel #555555ff

[Repeated 1 time(s)]

> color sel #545454ff

[Repeated 2 time(s)]

> color sel #535353ff

[Repeated 1 time(s)]

> color sel #525252ff

[Repeated 1 time(s)]

> color sel #515151ff

> color sel #505050ff

[Repeated 1 time(s)]

> color sel #4f4f4fff

[Repeated 2 time(s)]

> color sel #4e4e4eff

> color sel #4d4d4dff

[Repeated 2 time(s)]

> color sel #4c4c4cff

[Repeated 1 time(s)]

> color sel #4b4b4bff

[Repeated 2 time(s)]

> color sel #4a4a4aff

[Repeated 2 time(s)]

> color sel #494949ff

[Repeated 2 time(s)]

> color sel #484848ff

[Repeated 3 time(s)]

> color sel #474747ff

[Repeated 3 time(s)]

> color sel #464646ff

[Repeated 2 time(s)]

> color sel #454545ff

[Repeated 5 time(s)]

> color sel #464646ff

> color sel #474747ff

> color sel #494949ff

> color sel #4b4b4bff

> color sel #4c4c4cff

> color sel #4d4d4dff

> color sel #4e4e4eff

> color sel #505050ff

> color sel #515151ff

[Repeated 1 time(s)]

> color sel #525252ff

[Repeated 2 time(s)]

> color sel #535353ff

[Repeated 1 time(s)]

> color sel #545454ff

[Repeated 2 time(s)]

> color sel #555555ff

[Repeated 1 time(s)]

> color sel #565656ff

> color sel #575757ff

> color sel #585858ff

[Repeated 1 time(s)]

> color sel #595959ff

[Repeated 2 time(s)]

> color sel #5a5a5aff

[Repeated 2 time(s)]

> color sel #5b5b5bff

> color sel #5c5c5cff

> color sel #5f5f5fff

> color sel #606060ff

> color sel #626262ff

> color sel #646464ff

> color sel #656565ff

> color sel #676767ff

> color sel #696969ff

> color sel #6a6a6aff

> color sel #6c6c6cff

> color sel #6e6e6eff

> color sel #6f6f6fff

> color sel #717171ff

> color sel #737373ff

> color sel #757575ff

> color sel #767676ff

> color sel #787878ff

> color sel #797979ff

> color sel #7a7a7aff

> color sel #7b7b7bff

> color sel #7c7c7cff

> color sel #7d7d7dff

> color sel #7f7f7fff

> color sel #808080ff

> color sel #848484ff

> color sel #858585ff

> color sel #878787ff

> color sel #898989ff

> color sel #8a8a8aff

> color sel #8c8c8cff

> color sel #8e8e8eff

> color sel #8f8f8fff

> color sel #919191ff

> color sel #929292ff

> color sel #949494ff

> color sel #969696ff

> color sel #979797ff

> color sel #989898ff

> color sel #999999ff

[Repeated 2 time(s)]

> color sel #989898ff

> color sel #949494ff

> color sel #8a8a8aff

> color sel #838383ff

> color sel #7d7d7dff

> color sel #7a7a7aff

> color sel #777777ff

> color sel #747474ff

> color sel #717171ff

> color sel #6f6f6fff

> color sel #6d6d6dff

> color sel #6b6b6bff

> color sel #696969ff

> color sel #676767ff

> color sel #666666ff

> color sel #646464ff

> color sel #636363ff

> color sel #616161ff

> color sel #606060ff

> color sel #5f5f5fff

> color sel #5e5e5eff

[Repeated 2 time(s)]

> color sel #5d5d5dff

[Repeated 4 time(s)]

> color sel #5c5c5cff

[Repeated 1 time(s)]

> color sel #5b5b5bff

[Repeated 1 time(s)]

> color sel #5a5a5aff

[Repeated 2 time(s)]

> color sel #595959ff

[Repeated 1 time(s)]

> color sel #585858ff

[Repeated 3 time(s)]

> color sel #575757ff

[Repeated 3 time(s)]

> color sel #565656ff

[Repeated 3 time(s)]

> color sel #555555ff

[Repeated 2 time(s)]

> color sel #565656ff

> color sel #575757ff

> color sel #585858ff

> color sel #5a5a5aff

> color sel #5b5b5bff

> color sel #5c5c5cff

> color sel #5d5d5dff

> color sel #5e5e5eff

[Repeated 2 time(s)]

> color sel #5f5f5fff

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select add #17/C:87@MG

2 atoms, 2 residues, 2 models selected  

> distance #10/C:84@MG #17/C:87@MG

Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and V23_holo-coot-2.pdb
#17/C MG 87 MG: 3.390Å  

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select add #19/C:1@O3'

2 atoms, 2 residues, 2 models selected  

> distance #10/C:84@MG #19/C:1@O3'

Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and
Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/C G 1 O3': 7.687Å  

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select add #19/D:5@CA

2 atoms, 2 residues, 2 models selected  

> select #19/D:5@CA

1 atom, 1 residue, 1 model selected  

> select add #10/C:84@MG

2 atoms, 2 residues, 2 models selected  

> distance #19/D:5@CA #10/C:84@MG

Distance between Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb
#19/D CA 5 CA and V12_holo-coot-3.pdb #10/C MG 84 MG: 6.681Å  

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select add #19/D:6@CA

2 atoms, 2 residues, 2 models selected  

> distance #10/C:84@MG #19/D:6@CA

Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and
Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/D CA 6 CA: 2.783Å  

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select add #3/C:24@MG

2 atoms, 2 residues, 2 models selected  

> distance #10/C:84@MG #3/C:24@MG

Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and V4_holo-coot-3.pdb
#3/C MG 24 MG: 3.250Å  

> select #17/C:87@MG

1 atom, 1 residue, 1 model selected  

> select add #19/D:6@CA

2 atoms, 2 residues, 2 models selected  

> distance #17/C:87@MG #19/D:6@CA

Distance between V23_holo-coot-2.pdb #17/C MG 87 MG and
Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/D CA 6 CA: 5.916Å  

> select #17/C:87@MG

1 atom, 1 residue, 1 model selected  

> select add #19/C:1@O3'

2 atoms, 2 residues, 2 models selected  

> distance #17/C:87@MG #19/C:1@O3'

Distance between V23_holo-coot-2.pdb #17/C MG 87 MG and
Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/C G 1 O3': 4.880Å  

> select #17/C:87@MG

1 atom, 1 residue, 1 model selected  

> select add #19/D:5@CA

2 atoms, 2 residues, 2 models selected  

> distance #17/C:87@MG #19/D:5@CA

Distance between V23_holo-coot-2.pdb #17/C MG 87 MG and
Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/D CA 5 CA: 6.174Å  

> select #17/C:87@MG

1 atom, 1 residue, 1 model selected  

> select add #19/C:1@OP1

2 atoms, 2 residues, 2 models selected  

> distance #17/C:87@MG #19/C:1@OP1

Distance between V23_holo-coot-2.pdb #17/C MG 87 MG and
Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/C G 1 OP1: 6.874Å  

> select #19/D:5@CA

1 atom, 1 residue, 1 model selected  

> select add #19/C:1@OP1

2 atoms, 2 residues, 1 model selected  

> distance #19/D:5@CA #19/C:1@OP1

Distance between Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb
#19/D CA 5 CA and /C G 1 OP1: 2.234Å  

> select #19/D:7@CA

1 atom, 1 residue, 1 model selected  

> select add #19/C:1@OP2

2 atoms, 2 residues, 1 model selected  

> distance #19/D:7@CA #19/C:1@OP2

Distance between Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb
#19/D CA 7 CA and /C G 1 OP2: 2.625Å  

> ~distance #10/C:84@MG #17/C:87@MG

> ~distance #19/D:5@CA #10/C:84@MG

> ~distance #10/C:84@MG #19/C:1@O3'

> ~distance #19/D:7@CA #19/C:1@OP2

> ~distance #17/C:87@MG #19/C:1@O3'

> ~distance #19/D:5@CA #19/C:1@OP1

> ~distance #17/C:87@MG #19/C:1@OP1

> ~distance #10/C:84@MG #19/D:6@CA

> ~distance #17/C:87@MG #19/D:5@CA

> ~distance #10/C:84@MG #3/C:24@MG

> ~distance #17/C:87@MG #19/D:6@CA

> color sel #5f5f5fff

> color sel #5f5f5ffe

> color sel #5f5f5ffd

[Repeated 3 time(s)]

> color sel #5f5f5ffc

[Repeated 1 time(s)]

> color sel #5f5f5ffb

[Repeated 1 time(s)]

> color sel #5f5f5ffa

[Repeated 1 time(s)]

> color sel #5f5f5ff9

[Repeated 1 time(s)]

> color sel #5f5f5ff8

> color sel #5f5f5ff7

> color sel #5f5f5ff6

> color sel #5f5f5ff5

> color sel #5f5f5ff3

> color sel #5f5f5ff2

> color sel #5f5f5ff1

> color sel #5f5f5ff0

> color sel #5f5f5fee

> color sel #5f5f5fec

> color sel #5f5f5feb

> color sel #5f5f5fea

> color sel #5f5f5fe9

[Repeated 3 time(s)]

> color sel #5f5f5fe8

[Repeated 2 time(s)]

> color sel #5f5f5fe7

[Repeated 6 time(s)]

> select #19/C

1889 atoms, 2107 bonds, 89 residues, 1 model selected  

> lighting simple

> lighting soft

> lighting full

> lighting soft

> lighting simple

> lighting soft

> lighting simple

> color sel #5f5f5fe7

> color sel #5f5f5fe6

> color sel #5f5f5fe3

> color sel #5f5f5fe2

> color sel #5f5f5fe1

[Repeated 1 time(s)]

> color sel #5f5f5fe0

> color sel #5f5f5fdf

[Repeated 2 time(s)]

> color sel #5f5f5fde

[Repeated 1 time(s)]

> color sel #5f5f5fdd

> color sel #5f5f5fdc

> color sel #5f5f5fda

> color sel #5f5f5fd8

> color sel #5f5f5fd6

> color sel #5f5f5fd4

> color sel #5f5f5fd2

> color sel #5f5f5fd1

> color sel #5f5f5fd0

> color sel #5f5f5fcf

> color sel #5f5f5fcd

> color sel #5f5f5fcc

> color sel #5f5f5fca

> color sel #5f5f5fc9

> color sel #5f5f5fc7

> color sel #5f5f5fc5

> color sel #5f5f5fc1

> color sel #5f5f5fbf

> color sel #5f5f5fbd

> color sel #5f5f5fbb

> color sel #5f5f5fba

> color sel #5f5f5fb8

> color sel #5f5f5fb5

> color sel #5f5f5fb4

> color sel #5f5f5fb1

> color sel #5f5f5fb0

> color sel #5f5f5fae

[Repeated 2 time(s)]

> color sel #5f5f5fad

> color sel #5f5f5fac

> color sel #5f5f5fab

> color sel #5f5f5fa9

> color sel #5f5f5fa7

> color sel #5f5f5fa3

> color sel #5f5f5f9f

> color sel #5f5f5f9b

> color sel #5f5f5f99

> color sel #5f5f5f96

[Repeated 3 time(s)]

> color sel #5f5f5f95

> color sel #5f5f5f94

> color sel #5f5f5f93

> color sel #5f5f5f92

> color sel #5f5f5f90

> color sel #5f5f5f8f

> color sel #5f5f5f8e

> color sel #5f5f5f8d

> color sel #5f5f5f8c

[Repeated 1 time(s)]

> color sel #5f5f5f8b

> color sel #5f5f5f89

> color sel #5f5f5f88

[Repeated 1 time(s)]

> color sel #5f5f5f87

> color sel #5f5f5f85

> color sel #5f5f5f84

[Repeated 1 time(s)]

> color sel #5f5f5f83

[Repeated 2 time(s)]

> color sel #5f5f5f84

> color sel #5f5f5f87

> color sel #5f5f5f8d

> color sel #5f5f5f95

> color sel #5f5f5f99

> color sel #5f5f5f9d

> color sel #5f5f5f9f

> color sel #5f5f5fa1

> color sel #5f5f5fa3

> color sel #5f5f5fa4

> color sel #5f5f5fa5

[Repeated 2 time(s)]

> color sel #5f5f5fa6

> color sel #5f5f5fa8

> color sel #5f5f5fab

> color sel #5f5f5fad

> color sel #5f5f5fae

> color sel #5f5f5faf

[Repeated 2 time(s)]

> color sel #5f5f5fb1

> color sel #5f5f5fb2

> color sel #5f5f5fb5

> color sel #5f5f5fb6

> color sel #5f5f5fb7

[Repeated 1 time(s)]

> color sel #5f5f5fb8

[Repeated 2 time(s)]

> color sel #5f5f5fb9

[Repeated 1 time(s)]

> color sel #5f5f5fbb

> color sel #5f5f5fbd

> color sel #5f5f5fc1

> color sel #5f5f5fc7

> color sel #5f5f5fcc

> color sel #5f5f5fcf

> color sel #5f5f5fd0

> color sel #5f5f5fce

> color sel #5f5f5fc2

> color sel #5f5f5fb8

> color sel #5f5f5fb2

> color sel #5f5f5fb1

[Repeated 1 time(s)]

> color sel #5f5f5fb0

> color sel #5f5f5fad

> color sel #5f5f5fab

> color sel #5f5f5fa9

> color sel #5f5f5fa5

> color sel #5f5f5fa3

> select #19/D:30@CA

1 atom, 1 residue, 1 model selected  

> select add #19/D:5@CA

2 atoms, 2 residues, 1 model selected  

> color sel #404040ff

> select #19/D:7@CA

1 atom, 1 residue, 1 model selected  

> select #19/D:7@CA

1 atom, 1 residue, 1 model selected  

> color sel #404040ff

> color sel #3f3f3fff

> color sel #3e3e3eff

> color sel #3d3d3dff

[Repeated 4 time(s)]

> color sel #3c3c3cff

[Repeated 2 time(s)]

> color sel #3d3d3dff

[Repeated 1 time(s)]

> select #19/D:6@CA

1 atom, 1 residue, 1 model selected  

> select add #19/D:1@CA

2 atoms, 2 residues, 1 model selected  

> select add #19/D:3@CA

3 atoms, 3 residues, 1 model selected  

> color sel #4f8f00ff

> color sel #005493ff

> select clear

> save
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/apo_holo_analysis/ions/ions_holo_new_core_aa_models_ternary_comp.cxs

> hide #19 models

> save ions_core_holo.png supersample 3 transparentBackground true

> lighting simple

> lighting soft

> lighting simple

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> ui tool show "Side View"

> lighting soft

> lighting simple

> lighting soft

> save ions_core_holo_2.png supersample 3 transparentBackground true

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select add #11/A:390@OP2

2 atoms, 2 residues, 2 models selected  

> distance #10/C:84@MG #11/A:390@OP2

Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and V14_holo-coot-1.pdb
#11/A A 390 OP2: 3.278Å  

> select #6/C:24@MG

1 atom, 1 residue, 1 model selected  

> select add #6/A:390@OP2

2 atoms, 2 residues, 1 model selected  

> distance #6/C:24@MG #6/A:390@OP2

Distance between V7_holo-coot-2.pdb #6/C MG 24 MG and /A A 390 OP2: 4.213Å  

> select #6/C:24@MG

1 atom, 1 residue, 1 model selected  

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select clear

> select #17/C:87@MG

1 atom, 1 residue, 1 model selected  

> select add #11/A:390@OP2

2 atoms, 2 residues, 2 models selected  

> distance #17/C:87@MG #11/A:390@OP2

Distance between V23_holo-coot-2.pdb #17/C MG 87 MG and V14_holo-coot-1.pdb
#11/A A 390 OP2: 4.350Å  

> ~distance #6/C:24@MG #6/A:390@OP2

> ~distance #10/C:84@MG #11/A:390@OP2

> ~distance #17/C:87@MG #11/A:390@OP2

> select clear

> lighting simple

> toolshed show

> select #18/C:24@MG

1 atom, 1 residue, 1 model selected  

> select add #11/A:390@OP2

2 atoms, 2 residues, 2 models selected  

> distance #18/C:24@MG #11/A:390@OP2

Distance between V25_holo-coot-2.pdb #18/C MG 24 MG and V14_holo-coot-1.pdb
#11/A A 390 OP2: 4.140Å  

> select #17/A:50@OP2

1 atom, 1 residue, 1 model selected  

> select add #9/C:4@MG

2 atoms, 2 residues, 2 models selected  

> distance #17/A:50@OP2 #9/C:4@MG

Distance between V23_holo-coot-2.pdb #17/A A 50 OP2 and V11_holo-coot-1.pdb
#9/C MG 4 MG: 5.979Å  

> select #11/A:390@OP2

1 atom, 1 residue, 1 model selected  

> select add #10/C:84@MG

2 atoms, 2 residues, 2 models selected  

> distance #11/A:390@OP2 #10/C:84@MG

Distance between V14_holo-coot-1.pdb #11/A A 390 OP2 and V12_holo-coot-3.pdb
#10/C MG 84 MG: 3.278Å  

> select #17/C:87@MG

1 atom, 1 residue, 1 model selected  

> select add #10/C:84@MG

2 atoms, 2 residues, 2 models selected  

> distance #17/C:87@MG #10/C:84@MG

Distance between V23_holo-coot-2.pdb #17/C MG 87 MG and V12_holo-coot-3.pdb
#10/C MG 84 MG: 3.390Å  

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select add #17/C:87@MG

2 atoms, 2 residues, 2 models selected  

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> select #10/C:84@MG

1 atom, 1 residue, 1 model selected  

> color sel lime

> color sel purple

> ~distance #11/A:390@OP2 #10/C:84@MG

> ~distance #17/A:50@OP2 #9/C:4@MG

> ~distance #17/C:87@MG #10/C:84@MG

> ~distance #18/C:24@MG #11/A:390@OP2

> select clear

> select #7/C:24@MG

1 atom, 1 residue, 1 model selected  

> select add #7/A:390@C5'

2 atoms, 2 residues, 1 model selected  

> distance #7/C:24@MG #7/A:390@C5'

Distance between V9_holo-coot-0.pdb #7/C MG 24 MG and /A A 390 C5': 5.156Å  

> select clear

> select #7/C:24@MG

1 atom, 1 residue, 1 model selected  

> select add #11/A:390@OP2

2 atoms, 2 residues, 2 models selected  

> distance #7/C:24@MG #11/A:390@OP2

Distance between V9_holo-coot-0.pdb #7/C MG 24 MG and V14_holo-coot-1.pdb
#11/A A 390 OP2: 4.308Å  

> select #3/C:24@MG

1 atom, 1 residue, 1 model selected  

> select add #11/A:390@OP2

2 atoms, 2 residues, 2 models selected  

> distance #3/C:24@MG #11/A:390@OP2

Distance between V4_holo-coot-3.pdb #3/C MG 24 MG and V14_holo-coot-1.pdb
#11/A A 390 OP2: 4.180Å  

> select #13/C:24@MG

1 atom, 1 residue, 1 model selected  

> select #11/A:390@OP2

1 atom, 1 residue, 1 model selected  

> select add #13/C:24@MG

2 atoms, 2 residues, 2 models selected  

> distance #11/A:390@OP2 #13/C:24@MG

Distance between V14_holo-coot-1.pdb #11/A A 390 OP2 and V17_holo-coot-3.pdb
#13/C MG 24 MG: 4.168Å  

> select #4/C:24@MG

1 atom, 1 residue, 1 model selected  

> select add #11/A:390@OP2

2 atoms, 2 residues, 2 models selected  

> distance #4/C:24@MG #11/A:390@OP2

Distance between V5_holo-coot-1.pdb #4/C MG 24 MG and V14_holo-coot-1.pdb
#11/A A 390 OP2: 4.683Å  

> ~distance #7/C:24@MG #7/A:390@C5'

> ~distance #4/C:24@MG #11/A:390@OP2

> ~distance #3/C:24@MG #11/A:390@OP2

> ~distance #7/C:24@MG #11/A:390@OP2

> ~distance #11/A:390@OP2 #13/C:24@MG

> select clear

> save ions_core_holo_2.png supersample 3 transparentBackground true

> save
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/apo_holo_analysis/ions/ions_holo_new_core_aa_models.cxs

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V1_Mg-
> coot-1.pdb

Chain information for V1_Mg-coot-1.pdb #20  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V2_Mg-
> coot-1.pdb

Chain information for V2_Mg-coot-1.pdb #21  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V3_Mg-
> coot-2.pdb

Chain information for V3_Mg-coot-2.pdb #22  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V4_Mg-
> coot-2.pdb

Chain information for V4_Mg-coot-2.pdb #23  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V5_Mg-
> coot-1.pdb

Chain information for V5_Mg-coot-1.pdb #24  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V6_Mg-
> coot-1.pdb

Chain information for V6_Mg-coot-1.pdb #25  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V7_Mg-
> coot-2.pdb

Chain information for V7_Mg-coot-2.pdb #26  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V8_Mg-
> coot-2.pdb

Chain information for V8_Mg-coot-2.pdb #27  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V9_Mg-
> coot-3.pdb

Chain information for V9_Mg-coot-3.pdb #28  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V10_Mg-
> coot-3.pdb

Chain information for V10_Mg-coot-3.pdb #29  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V11_Mg-
> coot-2.pdb

Chain information for V11_Mg-coot-2.pdb #30  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V12_real_space_refined_011-coot-0.pdb

Chain information for V12_real_space_refined_011-coot-0.pdb #31  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V13_Mg-
> coot-2.pdb

Chain information for V13_Mg-coot-2.pdb #32  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V13_Mg-
> coot-3_6.pdb

Chain information for V13_Mg-coot-3_6.pdb #33  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V14_Mg-
> coot-1.pdb

Chain information for V14_Mg-coot-1.pdb #34  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V15_Mg-
> coot-2.pdb

Chain information for V15_Mg-coot-2.pdb #35  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V16_Mg-
> coot-1.pdb

Chain information for V16_Mg-coot-1.pdb #36  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V17_Mg-
> coot-2.pdb

Chain information for V17_Mg-coot-2.pdb #37  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V18_Mg-
> coot-1.pdb

Chain information for V18_Mg-coot-1.pdb #38  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V19_Mg-
> coot-3.pdb

Chain information for V19_Mg-coot-3.pdb #39  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V20_Mg-
> coot-2.pdb

Chain information for V20_Mg-coot-2.pdb #40  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V21_Mg_real_space_refined_002-coot-1.pdb

Chain information for V21_Mg_real_space_refined_002-coot-1.pdb #41  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V22_Mg_6sig.pdb

Chain information for V22_Mg_6sig.pdb #42  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V22_Mg_real_space_refined_002-coot-1.pdb

Chain information for V22_Mg_real_space_refined_002-coot-1.pdb #43  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V23_Mg_6sig.pdb

Chain information for V23_Mg_6sig.pdb #44  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V23_Mg-
> coot-1.pdb

Chain information for V23_Mg-coot-1.pdb #45  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V24_6sig.pdb

Chain information for V24_6sig.pdb #46  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V24_Mg-
> coot-6.pdb

Chain information for V24_Mg-coot-6.pdb #47  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V25_Mg-
> coot-1.pdb

Chain information for V25_Mg-coot-1.pdb #48  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V26_Mg-
> coot-1.pdb

Chain information for V26_Mg-coot-1.pdb #49  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V27_Mg-
> coot-2.pdb

Chain information for V27_Mg-coot-2.pdb #50  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V28_Mg-
> coot-1.pdb

Chain information for V28_Mg-coot-1.pdb #51  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V29_Mg-
> coot-2.pdb

Chain information for V29_Mg-coot-2.pdb #52  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V30_Mg-
> coot-3.pdb

Chain information for V30_Mg-coot-3.pdb #53  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V31_Mg-
> coot-3.pdb

Chain information for V31_Mg-coot-3.pdb #54  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V32_Mg-
> coot-2.pdb

Chain information for V32_Mg-coot-2.pdb #55  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V33_Mg-
> coot-2.pdb

Chain information for V33_Mg-coot-2.pdb #56  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V34_Mg-
> coot-3.pdb

Chain information for V34_Mg-coot-3.pdb #57  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V35_Mg-
> coot-2.pdb

Chain information for V35_Mg-coot-2.pdb #58  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V36_Mg-
> coot-1.pdb

Chain information for V36_Mg-coot-1.pdb #59  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V37_Mg-
> coot-1.pdb

Chain information for V37_Mg-coot-1.pdb #60  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V38_Mg-
> coot-1.pdb

Chain information for V38_Mg-coot-1.pdb #61  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V39_Mg_real_space_refined_002-coot-0.pdb

Chain information for V39_Mg_real_space_refined_002-coot-0.pdb #62  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V40_Mg_real_space_refined_003-coot-0_aligned.pdb

Chain information for V40_Mg_real_space_refined_003-coot-0_aligned.pdb #63  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V40_Mg_real_space_refined_003-coot-0.pdb

Chain information for V40_Mg_real_space_refined_003-coot-0.pdb #64  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V41_Mg_real_space_refined_003-coot-0.pdb

Chain information for V41_Mg_real_space_refined_003-coot-0.pdb #65  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V42_Mg_real_space_refined_003-coot-0.pdb

Chain information for V42_Mg_real_space_refined_003-coot-0.pdb #66  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V43_Mg_real_space_refined_001-coot-0.pdb

Chain information for V43_Mg_real_space_refined_001-coot-0.pdb #67  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V44_Mg_real_space_refined_003-coot-0.pdb

Chain information for V44_Mg_real_space_refined_003-coot-0.pdb #68  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V45_Mg-
> coot-3.pdb

Chain information for V45_Mg-coot-3.pdb #69  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V46_Mg-
> coot-2.pdb

Chain information for V46_Mg-coot-2.pdb #70  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V47_Mg-
> coot-4.pdb

Chain information for V47_Mg-coot-4.pdb #71  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V48_Mg-
> coot-1.pdb

Chain information for V48_Mg-coot-1.pdb #72  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V49_Mg-
> coot-2.pdb

Chain information for V49_Mg-coot-2.pdb #73  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  
[Repeated 53 time(s)]

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V1_holo_set_noprot-
> coot-2.pdb

Chain information for V1_holo_set_noprot-coot-2.pdb #74  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V8_holo_no_prot_a-
> coot-4.pdb

Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V8_holo_no_prot_a-
coot-4.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ASN B 10 GLN B 19 1 10  
Start residue of secondary structure not found: HELIX 2 2 ALA B 54 GLU B 70 1
17  
Start residue of secondary structure not found: HELIX 3 3 GLN B 87 ALA B 89 1
3  
Start residue of secondary structure not found: HELIX 4 4 TYR B 94 LYS B 107 1
14  
Start residue of secondary structure not found: SHEET 1 1 1 PHE B 28 ASP B 34
0  
2 messages similar to the above omitted  
  
Chain information for V8_holo_no_prot_a-coot-4.pdb #75  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V13_holo_set_noapo-
> coot-3.pdb

Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V13_holo_set_noapo-
coot-3.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ASN B 10 GLN B 19 1 10  
Start residue of secondary structure not found: HELIX 2 2 ALA B 54 GLU B 70 1
17  
Start residue of secondary structure not found: HELIX 3 3 GLN B 87 ALA B 89 1
3  
Start residue of secondary structure not found: HELIX 4 4 TYR B 94 LYS B 107 1
14  
Start residue of secondary structure not found: SHEET 1 1 1 PHE B 28 ASP B 34
0  
2 messages similar to the above omitted  
  
Chain information for V13_holo_set_noapo-coot-3.pdb #76  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V20_holo_no_prot-
> coot-1.pdb

Chain information for V20_holo_no_prot-coot-1.pdb #77  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V22_holo_no_prot-
> coot-1.pdb

Chain information for V22_holo_no_prot-coot-1.pdb #78  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V24_holo_no_prot-
> coot-3.pdb

Chain information for V24_holo_no_prot-coot-3.pdb #79  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  
[Repeated 5 time(s)]

> select
> #1/A:15,21-29,39-67,69-84,96-101,105-112,249-261,272-293,295-312,327-340,386-400

3255 atoms, 3639 bonds, 151 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #20-49,51-79#!50 to #1 & sel matrix Nucleic

Computing secondary structure  
[Repeated 60 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V1_Mg-coot-1.pdb, chain A
(#20), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.460 angstroms; (across all 151 pairs:
0.510)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V2_Mg-coot-1.pdb, chain A
(#21), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.443 angstroms; (across all 151 pairs:
0.490)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V3_Mg-coot-2.pdb, chain A
(#22), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.478 angstroms; (across all 151 pairs:
0.530)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V4_Mg-coot-2.pdb, chain A
(#23), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.470 angstroms; (across all 151 pairs:
0.515)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V5_Mg-coot-1.pdb, chain A
(#24), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.472 angstroms; (across all 151 pairs:
0.521)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V6_Mg-coot-1.pdb, chain A
(#25), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.469 angstroms; (across all 151 pairs:
0.519)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V7_Mg-coot-2.pdb, chain A
(#26), sequence alignment score = 604  
RMSD between 148 pruned atom pairs is 0.517 angstroms; (across all 151 pairs:
0.622)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V8_Mg-coot-2.pdb, chain A
(#27), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.465 angstroms; (across all 151 pairs:
0.504)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V9_Mg-coot-3.pdb, chain A
(#28), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.490 angstroms; (across all 151 pairs:
0.523)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V10_Mg-coot-3.pdb, chain A
(#29), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.491 angstroms; (across all 151 pairs:
0.532)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V11_Mg-coot-2.pdb, chain A
(#30), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.480 angstroms; (across all 151 pairs:
0.536)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
V12_real_space_refined_011-coot-0.pdb, chain A (#31), sequence alignment score
= 604  
RMSD between 150 pruned atom pairs is 0.523 angstroms; (across all 151 pairs:
0.559)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V13_Mg-coot-2.pdb, chain A
(#32), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.504 angstroms; (across all 151 pairs:
0.540)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V13_Mg-coot-3_6.pdb, chain A
(#33), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.504 angstroms; (across all 151 pairs:
0.540)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V14_Mg-coot-1.pdb, chain A
(#34), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.477 angstroms; (across all 151 pairs:
0.534)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V15_Mg-coot-2.pdb, chain A
(#35), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.461 angstroms; (across all 151 pairs:
0.518)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V16_Mg-coot-1.pdb, chain A
(#36), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.452 angstroms; (across all 151 pairs:
0.506)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V17_Mg-coot-2.pdb, chain A
(#37), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.439 angstroms; (across all 151 pairs:
0.502)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V18_Mg-coot-1.pdb, chain A
(#38), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.461 angstroms; (across all 151 pairs:
0.498)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V19_Mg-coot-3.pdb, chain A
(#39), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.458 angstroms; (across all 151 pairs:
0.496)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V20_Mg-coot-2.pdb, chain A
(#40), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.458 angstroms; (across all 151 pairs:
0.520)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
V21_Mg_real_space_refined_002-coot-1.pdb, chain A (#41), sequence alignment
score = 604  
RMSD between 150 pruned atom pairs is 0.480 angstroms; (across all 151 pairs:
0.525)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V22_Mg_6sig.pdb, chain A
(#42), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.449 angstroms; (across all 151 pairs:
0.508)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
V22_Mg_real_space_refined_002-coot-1.pdb, chain A (#43), sequence alignment
score = 604  
RMSD between 150 pruned atom pairs is 0.449 angstroms; (across all 151 pairs:
0.508)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V23_Mg_6sig.pdb, chain A
(#44), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.495 angstroms; (across all 151 pairs:
0.534)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V23_Mg-coot-1.pdb, chain A
(#45), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.495 angstroms; (across all 151 pairs:
0.534)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V24_6sig.pdb, chain A (#46),
sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.487 angstroms; (across all 151 pairs:
0.552)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V24_Mg-coot-6.pdb, chain A
(#47), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.487 angstroms; (across all 151 pairs:
0.552)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V25_Mg-coot-1.pdb, chain A
(#48), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.465 angstroms; (across all 151 pairs:
0.518)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V26_Mg-coot-1.pdb, chain A
(#49), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.491 angstroms; (across all 151 pairs:
0.546)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V28_Mg-coot-1.pdb, chain A
(#51), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.514 angstroms; (across all 151 pairs:
0.557)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V29_Mg-coot-2.pdb, chain A
(#52), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.486 angstroms; (across all 151 pairs:
0.512)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V30_Mg-coot-3.pdb, chain A
(#53), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.427 angstroms; (across all 151 pairs:
0.470)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V31_Mg-coot-3.pdb, chain A
(#54), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.462 angstroms; (across all 151 pairs:
0.524)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V32_Mg-coot-2.pdb, chain A
(#55), sequence alignment score = 604  
RMSD between 149 pruned atom pairs is 0.454 angstroms; (across all 151 pairs:
0.624)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V33_Mg-coot-2.pdb, chain A
(#56), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.472 angstroms; (across all 151 pairs:
0.515)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V34_Mg-coot-3.pdb, chain A
(#57), sequence alignment score = 604  
RMSD between 149 pruned atom pairs is 0.539 angstroms; (across all 151 pairs:
0.609)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V35_Mg-coot-2.pdb, chain A
(#58), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.538 angstroms; (across all 151 pairs:
0.577)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V36_Mg-coot-1.pdb, chain A
(#59), sequence alignment score = 604  
RMSD between 149 pruned atom pairs is 0.505 angstroms; (across all 151 pairs:
0.589)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V37_Mg-coot-1.pdb, chain A
(#60), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.476 angstroms; (across all 151 pairs:
0.520)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V38_Mg-coot-1.pdb, chain A
(#61), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.462 angstroms; (across all 151 pairs:
0.509)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
V39_Mg_real_space_refined_002-coot-0.pdb, chain A (#62), sequence alignment
score = 604  
RMSD between 150 pruned atom pairs is 0.495 angstroms; (across all 151 pairs:
0.539)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
V40_Mg_real_space_refined_003-coot-0_aligned.pdb, chain A (#63), sequence
alignment score = 604  
RMSD between 149 pruned atom pairs is 0.522 angstroms; (across all 151 pairs:
0.591)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
V40_Mg_real_space_refined_003-coot-0.pdb, chain A (#64), sequence alignment
score = 604  
RMSD between 149 pruned atom pairs is 0.526 angstroms; (across all 151 pairs:
0.595)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
V41_Mg_real_space_refined_003-coot-0.pdb, chain A (#65), sequence alignment
score = 604  
RMSD between 150 pruned atom pairs is 0.484 angstroms; (across all 151 pairs:
0.540)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
V42_Mg_real_space_refined_003-coot-0.pdb, chain A (#66), sequence alignment
score = 604  
RMSD between 150 pruned atom pairs is 0.482 angstroms; (across all 151 pairs:
0.526)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
V43_Mg_real_space_refined_001-coot-0.pdb, chain A (#67), sequence alignment
score = 604  
RMSD between 149 pruned atom pairs is 0.513 angstroms; (across all 151 pairs:
0.602)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
V44_Mg_real_space_refined_003-coot-0.pdb, chain A (#68), sequence alignment
score = 604  
RMSD between 150 pruned atom pairs is 0.507 angstroms; (across all 151 pairs:
0.549)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V45_Mg-coot-3.pdb, chain A
(#69), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.494 angstroms; (across all 151 pairs:
0.546)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V46_Mg-coot-2.pdb, chain A
(#70), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.436 angstroms; (across all 151 pairs:
0.490)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V47_Mg-coot-4.pdb, chain A
(#71), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.564 angstroms; (across all 151 pairs:
0.596)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V48_Mg-coot-1.pdb, chain A
(#72), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.468 angstroms; (across all 151 pairs:
0.523)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V49_Mg-coot-2.pdb, chain A
(#73), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.461 angstroms; (across all 151 pairs:
0.529)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V1_holo_set_noprot-
coot-2.pdb, chain A (#74), sequence alignment score = 604  
RMSD between 149 pruned atom pairs is 0.402 angstroms; (across all 151 pairs:
0.464)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V8_holo_no_prot_a-coot-4.pdb,
chain A (#75), sequence alignment score = 604  
RMSD between 149 pruned atom pairs is 0.486 angstroms; (across all 151 pairs:
0.562)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V13_holo_set_noapo-
coot-3.pdb, chain A (#76), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.491 angstroms; (across all 151 pairs:
0.491)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V20_holo_no_prot-coot-1.pdb,
chain A (#77), sequence alignment score = 604  
RMSD between 151 pruned atom pairs is 0.442 angstroms; (across all 151 pairs:
0.442)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V22_holo_no_prot-coot-1.pdb,
chain A (#78), sequence alignment score = 604  
RMSD between 149 pruned atom pairs is 0.357 angstroms; (across all 151 pairs:
0.438)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V24_holo_no_prot-coot-3.pdb,
chain A (#79), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.494 angstroms; (across all 151 pairs:
0.557)  
  
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V27_Mg-coot-2.pdb, chain A
(#50), sequence alignment score = 604  
RMSD between 150 pruned atom pairs is 0.544 angstroms; (across all 151 pairs:
0.594)  
  

> select #20-79/A

537720 atoms, 602280 bonds, 25020 residues, 60 models selected  

> color sel dim gray

> hide sel target a

> select #20-79/A:50,389,390

3960 atoms, 4380 bonds, 180 residues, 60 models selected  

> cartoon hide sel

> show sel target ab

> nucleotides sel atoms

> style nucleic & sel stick

Changed 3960 atom styles  

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> ui tool show "Color Actions"

> color sel cornflower blue

> hide #19#!1-18 target m

> select #20/C:1@O

1 atom, 1 residue, 1 model selected  

> select add #42/B:67@MG

2 atoms, 2 residues, 2 models selected  

> select add #61/B:65@MG

3 atoms, 3 residues, 3 models selected  

> select add #65/B:44@MG

4 atoms, 4 residues, 4 models selected  

> hide sel target a

> select #30/B:61@MG

1 atom, 1 residue, 1 model selected  

> select add #69/B:62@MG

2 atoms, 2 residues, 2 models selected  

> hide sel target a

> select #20-79/B

2199 atoms, 1 pseudobond, 2199 residues, 56 models selected  

> ui tool show "Selection Inspector"

> size sel atomRadius 0.7

Changed 2199 atom radii  

> select clear

> select #46/B:66@MG

1 atom, 1 residue, 1 model selected  

> select add #75/A:390@O3'

2 atoms, 2 residues, 2 models selected  

> distance #46/B:66@MG #75/A:390@O3'

Distance between V24_6sig.pdb #46/B MG 66 MG and V8_holo_no_prot_a-coot-4.pdb
#75/A A 390 O3': 5.502Å  

> close #42

> close #44

> close #46

> select #20-79/B

2062 atoms, 1 pseudobond, 2062 residues, 53 models selected  

> close #33

> close #63

> select #20-79/B:7

50 atoms, 50 residues, 50 models selected  

> select #75/C:7@MG

1 atom, 1 residue, 1 model selected  

> select add #69/B:7@MG

2 atoms, 2 residues, 2 models selected  

> select add #68/B:7@MG

3 atoms, 3 residues, 3 models selected  

> select add #55/B:7@MG

4 atoms, 4 residues, 4 models selected  

> select #20-79/B

1987 atoms, 1 pseudobond, 1987 residues, 51 models selected  

> select #20-79/C

187 atoms, 187 residues, 6 models selected  

> ui tool show "Selection Inspector"

> size sel atomRadius 0.7

Changed 187 atom radii  

> select #20-79/B:7

50 atoms, 50 residues, 50 models selected  

> ui tool show "Color Actions"

> color sel #941100ff

> select #20-79/C:7

5 atoms, 5 residues, 5 models selected  

> ui tool show "Color Actions"

> select #20-79/C:7

5 atoms, 5 residues, 5 models selected  

> ui tool show "Color Actions"

> color sel #4f8f00ff

> color sel #941100ff

> select #20-79/B

1987 atoms, 1 pseudobond, 1987 residues, 51 models selected  

> ui tool show "Color Actions"

> color sel forest green

> select #20-79/C

187 atoms, 187 residues, 6 models selected  

> ui tool show "Color Actions"

> color sel forest green

> select #20-79/C:7

5 atoms, 5 residues, 5 models selected  

> ui tool show "Color Actions"

> select #20-79/B:7

50 atoms, 50 residues, 50 models selected  

> ui tool show "Color Actions"

> color sel #945200ff

> color sel #941100ff

> select #20-79/C:7

5 atoms, 5 residues, 5 models selected  

> ui tool show "Color Actions"

> color sel #945200ff

> color sel #941100ff

> select clear

> select #20-79/B:57

21 atoms, 21 residues, 21 models selected  

> select #20-79/B:57,66

35 atoms, 35 residues, 25 models selected  

> select clear

> select #65/B:41@MG

1 atom, 1 residue, 1 model selected  

> select add #39/B:64@MG

2 atoms, 2 residues, 2 models selected  

> select add #41/B:62@MG

3 atoms, 3 residues, 3 models selected  

> select add #43/B:63@MG

4 atoms, 4 residues, 4 models selected  

> select subtract #43/B:63@MG

3 atoms, 3 residues, 3 models selected  

> select add #43/B:63@MG

4 atoms, 4 residues, 4 models selected  

> select subtract #41/B:62@MG

3 atoms, 3 residues, 3 models selected  

> select add #31/B:58@MG

4 atoms, 4 residues, 4 models selected  

> select add #30/B:57@MG

5 atoms, 5 residues, 5 models selected  

> select subtract #31/B:58@MG

4 atoms, 4 residues, 4 models selected  

> select subtract #65/B:41@MG

3 atoms, 3 residues, 3 models selected  

> select add #65/B:41@MG

4 atoms, 4 residues, 4 models selected  

> select add #31/B:58@MG

5 atoms, 5 residues, 5 models selected  

> select subtract #31/B:58@MG

4 atoms, 4 residues, 4 models selected  

> select subtract #39/B:64@MG

3 atoms, 3 residues, 3 models selected  

> select add #39/B:64@MG

4 atoms, 4 residues, 4 models selected  

> select add #38/B:61@MG

5 atoms, 5 residues, 5 models selected  

> select add #36/B:60@MG

6 atoms, 6 residues, 6 models selected  

> select subtract #43/B:63@MG

5 atoms, 5 residues, 5 models selected  

> select add #43/B:63@MG

6 atoms, 6 residues, 6 models selected  

> hide sel target a

> select #26/B:49@MG

1 atom, 1 residue, 1 model selected  

> select add #31/B:58@MG

2 atoms, 2 residues, 2 models selected  

> select add #41/B:62@MG

3 atoms, 3 residues, 3 models selected  

> select add #34/B:59@MG

4 atoms, 4 residues, 4 models selected  

> hide sel target a

> select #43/B:65@MG

1 atom, 1 residue, 1 model selected  

> select add #30/B:60@MG

2 atoms, 2 residues, 2 models selected  

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> select #50/B:64@MG

1 atom, 1 residue, 1 model selected  

> select add #35/B:62@MG

2 atoms, 2 residues, 2 models selected  

> select add #51/B:68@MG

3 atoms, 3 residues, 3 models selected  

> select add #69/B:57@MG

4 atoms, 4 residues, 4 models selected  

> select add #62/B:45@MG

5 atoms, 5 residues, 5 models selected  

> select add #64/B:42@MG

6 atoms, 6 residues, 6 models selected  

> select add #27/B:54@MG

7 atoms, 7 residues, 7 models selected  

> select add #59/B:66@MG

8 atoms, 8 residues, 8 models selected  

> hide sel target a

> show sel target ab

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> select #21/B:38@MG

1 atom, 1 residue, 1 model selected  

> select add #30/B:38@MG

2 atoms, 2 residues, 2 models selected  

> select add #26/B:38@MG

3 atoms, 3 residues, 3 models selected  

> select #26/B:38@MG

1 atom, 1 residue, 1 model selected  

> select add #59/B:64@MG

2 atoms, 2 residues, 2 models selected  

> distance #26/B:38@MG #59/B:64@MG

Distance between V7_Mg-coot-2.pdb #26/B MG 38 MG and V36_Mg-coot-1.pdb #59/B
MG 64 MG: 9.452Å  

> select #26/B:38@MG

1 atom, 1 residue, 1 model selected  

> select add #23/B:7@MG

2 atoms, 2 residues, 2 models selected  

> distance #26/B:38@MG #23/B:7@MG

Distance between V7_Mg-coot-2.pdb #26/B MG 38 MG and V4_Mg-coot-2.pdb #23/B MG
7 MG: 8.150Å  

> select #26/B:38@MG

1 atom, 1 residue, 1 model selected  

> select add #21/B:38@MG

2 atoms, 2 residues, 2 models selected  

> select add #30/B:38@MG

3 atoms, 3 residues, 3 models selected  

> hide sel target a

> select #36/B:38@MG

1 atom, 1 residue, 1 model selected  

> select add #59/B:38@MG

2 atoms, 2 residues, 2 models selected  

> hide sel target a

> select add #62/B:30@MG

3 atoms, 3 residues, 3 models selected  

> select #53/B:65@MG

1 atom, 1 residue, 1 model selected  

> select #75/A:390@O3'

1 atom, 1 residue, 1 model selected  

> select add #24/B:50@MG

2 atoms, 2 residues, 2 models selected  

> distance #75/A:390@O3' #24/B:50@MG

Distance between V8_holo_no_prot_a-coot-4.pdb #75/A A 390 O3' and V5_Mg-
coot-1.pdb #24/B MG 50 MG: 5.771Å  

> select #24/B:50@MG

1 atom, 1 residue, 1 model selected  

> select #47/B:66@MG

1 atom, 1 residue, 1 model selected  

> select add #34/B:61@MG

2 atoms, 2 residues, 2 models selected  

> select add #32/B:60@MG

3 atoms, 3 residues, 3 models selected  

> select add #24/B:50@MG

4 atoms, 4 residues, 4 models selected  

> select add #53/B:65@MG

5 atoms, 5 residues, 5 models selected  

> select add #48/B:69@MG

6 atoms, 6 residues, 6 models selected  

> select add #36/B:61@MG

7 atoms, 7 residues, 7 models selected  

> select #47/B:66@MG

1 atom, 1 residue, 1 model selected  

> select add #55/B:62@MG

2 atoms, 2 residues, 2 models selected  

> distance #47/B:66@MG #55/B:62@MG

Distance between V24_Mg-coot-6.pdb #47/B MG 66 MG and V32_Mg-coot-2.pdb #55/B
MG 62 MG: 5.257Å  

> save
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/apo_holo_analysis/ions/ions_apo_holo_new_core_aa_models.cxs

> select #43/B:65@MG

1 atom, 1 residue, 1 model selected  

> select add #58/B:4@MG

2 atoms, 2 residues, 2 models selected  

> distance #43/B:65@MG #58/B:4@MG

Distance between V22_Mg_real_space_refined_002-coot-1.pdb #43/B MG 65 MG and
V35_Mg-coot-2.pdb #58/B MG 4 MG: 9.512Å  

> select #43/B:65@MG

1 atom, 1 residue, 1 model selected  

> select add #30/B:60@MG

2 atoms, 2 residues, 2 models selected  

> hide sel target a

> save
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/apo_holo_analysis/ions/ions_apo_holo_new_core_aa_models.cxs

> select #59/B:64@MG

1 atom, 1 residue, 1 model selected  

> select clear

> select #48/B:30@MG

1 atom, 1 residue, 1 model selected  

> select add #75/C:7@MG

2 atoms, 2 residues, 2 models selected  

> distance #48/B:30@MG #75/C:7@MG

Distance between V25_Mg-coot-1.pdb #48/B MG 30 MG and V8_holo_no_prot_a-
coot-4.pdb #75/C MG 7 MG: 7.041Å  

> select #48/B:30@MG

1 atom, 1 residue, 1 model selected  

> select add #58/A:389@OP1

2 atoms, 2 residues, 2 models selected  

> distance #48/B:30@MG #58/A:389@OP1

Distance between V25_Mg-coot-1.pdb #48/B MG 30 MG and V35_Mg-coot-2.pdb #58/A
A 389 OP1: 2.362Å  

> select #69/B:30@MG

1 atom, 1 residue, 1 model selected  

> select add #65/B:30@MG

2 atoms, 2 residues, 2 models selected  

> select add #48/B:30@MG

3 atoms, 3 residues, 3 models selected  

> select add #41/B:30@MG

4 atoms, 4 residues, 4 models selected  

> select add #55/B:66@MG

5 atoms, 5 residues, 5 models selected  

> select add #50/B:30@MG

6 atoms, 6 residues, 6 models selected  

> color sel blue

> select clear

> select #39/B:65@MG

1 atom, 1 residue, 1 model selected  

> select add #75/A:390@O3'

2 atoms, 2 residues, 2 models selected  

> distance #39/B:65@MG #75/A:390@O3'

Distance between V19_Mg-coot-3.pdb #39/B MG 65 MG and V8_holo_no_prot_a-
coot-4.pdb #75/A A 390 O3': 4.560Å  

> select #28/B:40@MG

1 atom, 1 residue, 1 model selected  

> select #75/A:390@O3'

1 atom, 1 residue, 1 model selected  

> select add #72/B:40@MG

2 atoms, 2 residues, 2 models selected  

> distance #75/A:390@O3' #72/B:40@MG

Distance between V8_holo_no_prot_a-coot-4.pdb #75/A A 390 O3' and V48_Mg-
coot-1.pdb #72/B MG 40 MG: 5.512Å  

> select #20-79/B:40

33 atoms, 33 residues, 33 models selected  

> save
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/apo_holo_analysis/ions/ions_apo_holo_new_core_aa_models.cxs

——— End of log from Wed Sep 17 17:35:30 2025 ———

opened ChimeraX session  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,6
      Model Number: Z1760005VLL/A
      Chip: Apple M2 Max
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 64 GB
      System Firmware Version: 11881.140.96
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.6.1 (24G90)
      Kernel Version: Darwin 24.6.0
      Time since boot: 1 day, 18 hours, 31 minutes

Graphics/Displays:

    Apple M2 Max:

      Chipset Model: Apple M2 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 38
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL P2715Q:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported
        DELL P2715Q:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMalign: 0.1.3
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-QScore: 1.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    finufft: 2.4.1
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13

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