id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
16912	ChimeraX bug report submission	hrishikesh.das@…		"{{{
The following bug report has been submitted:
Platform:        macOS-15.3.1-x86_64-i386-64bit
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 0x00007ff845e54b00 (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.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.dssp._dssp, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.alignment_algs._sw, chimerax.alignment_algs._nw, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct (total: 124)


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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/hrishikeshdas/Downloads/cryosparc_P70_J763_class_00_00082_volume.mrc

Opened cryosparc_P70_J763_class_00_00082_volume.mrc as #1, grid size
128,128,128, pixel 2.38, shown at level 0.175, step 1, values float32  

> volume #1 level 0.2605

> volume #1 level 0.3148

> open /Users/hrishikeshdas/Downloads/cryosparc_P70_J776_008_volume_map.mrc

Opened cryosparc_P70_J776_008_volume_map.mrc as #2, grid size 300,300,300,
pixel 1.02, shown at level 0.035, step 2, values float32  

> volume #2 level 0.07536

> lighting soft

> volume #2 level 0.08421

> volume #2 step 1

> volume #2 level 0.1129

> volume #2 level 0.1262

> volume #2 level 0.1384

> volume #2 level 0.1446

> volume #2 level 0.1794

> volume #2 level 0.1139

> volume #2 level 0.08728

> volume #2 level 0.1016

> volume #2 level 0.1067

> view

> open
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD5/Structures_FAST5/FAST5-trimer/trimer_fit.pdb

Summary of feedback from opening
/Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD5/Structures_FAST5/FAST5-trimer/trimer_fit.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLU A 57 GLU A 61 1 5  
Start residue of secondary structure not found: HELIX 2 2 ASN A 68 GLN A 74 1
7  
Start residue of secondary structure not found: HELIX 3 3 PRO A 77 VAL A 81 1
5  
Start residue of secondary structure not found: HELIX 4 4 VAL A 95 VAL A 107 1
13  
Start residue of secondary structure not found: HELIX 5 5 ALA A 114 LYS A 123
1 10  
15 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 21 21 LEU A 269 LYS A 281
1 13  
Start residue of secondary structure not found: HELIX 22 22 GLU A 288 ALA A
298 1 11  
Start residue of secondary structure not found: HELIX 23 23 CYS A 299 HIS A
304 1 6  
Start residue of secondary structure not found: HELIX 24 24 SER A 307 THR A
320 1 14  
Start residue of secondary structure not found: HELIX 25 25 ILE A 325 ILE A
334 1 10  
Start residue of secondary structure not found: HELIX 26 26 ALA A 335 GLN A
337 1 3  
12 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 39 39 LYS A 461 GLU A 478
1 18  
Start residue of secondary structure not found: HELIX 40 40 THR A 489 ASN A
508 1 20  
Start residue of secondary structure not found: HELIX 41 41 PRO A 511 LEU A
524 1 14  
Start residue of secondary structure not found: HELIX 42 42 PRO A 527 TYR A
529 1 3  
Start residue of secondary structure not found: HELIX 43 43 PRO A 563 VAL A
567 1 5  
Start residue of secondary structure not found: HELIX 44 44 ASP A 581 LYS A
589 1 9  
3 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 48 48 LEU A 697 LYS A 699
1 3  
Start residue of secondary structure not found: HELIX 49 49 ARG A 702 THR A
715 1 14  
Start residue of secondary structure not found: SHEET 1 1 1 LYS A 531 HIS A
533 0  
Start residue of secondary structure not found: SHEET 2 2 1 ASP A 543 LEU A
548 0  
Start residue of secondary structure not found: SHEET 3 3 1 MET A 649 PHE A
655 0  
Start residue of secondary structure not found: SHEET 4 4 1 TYR A 684 LEU A
689 0  
  
Chain information for trimer_fit.pdb  
---  
Chain | Description  
3.1/A 3.2/A | No description available  
3.3/A | No description available  
3.1/D 3.2/D | No description available  
  
Computing secondary structure  

> ui tool show ""Fit in Map""

> fitmap #3.1 inMap #1

Fit molecule trimer_fit.pdb (#3.1) to map
cryosparc_P70_J763_class_00_00082_volume.mrc (#1) using 5927 atoms  
average map value = 0.2425, steps = 76  
shifted from previous position = 13.2  
rotated from previous position = 6.09 degrees  
atoms outside contour = 3784, contour level = 0.31483  
  
Position of trimer_fit.pdb (#3.1) relative to
cryosparc_P70_J763_class_00_00082_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99729341 -0.03122240 -0.06656593 20.29814582  
0.02602687 0.99664965 -0.07753762 4.67634168  
0.06876383 0.07559526 0.99476474 -8.89332490  
Axis 0.72154427 -0.63765804 0.26975191  
Axis point 0.00000000 159.68100316 129.60582224  
Rotation angle (degrees) 6.09139195  
Shift along axis 9.26511246  
  

> undo

> color bychain

> color byhetero

> rainbow

> color bypolymer

> close #3

> open
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD5/Structures_FAST5/FAST5-trimer/F5_J398-a-b-
> c-coot-2.pdb

Chain information for F5_J398-a-b-c-coot-2.pdb #3  
---  
Chain | Description  
A | No description available  
B D | No description available  
  

> dssp

Computing secondary structure  

> fitmap #3 inMap #2

Fit molecule F5_J398-a-b-c-coot-2.pdb (#3) to map
cryosparc_P70_J776_008_volume_map.mrc (#2) using 14247 atoms  
average map value = 0.0697, steps = 280  
shifted from previous position = 29.6  
rotated from previous position = 24.7 degrees  
atoms outside contour = 10794, contour level = 0.10672  
  
Position of F5_J398-a-b-c-coot-2.pdb (#3) relative to
cryosparc_P70_J776_008_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.91950048 -0.02894727 0.39202159 -16.20378507  
-0.02973498 0.98930541 0.14279575 7.59306784  
-0.39196262 -0.14295752 0.90880606 90.62617398  
Axis -0.34244997 0.93953559 -0.00094400  
Axis point 213.96298040 0.00000000 74.26561963  
Rotation angle (degrees) 24.65913573  
Shift along axis 12.59739178  
  

> volume #2 level 0.1141

> volume #2 style image

> volume #2 style mesh

> volume #2 color #b2ffb2

> volume #2 color #b2b2b2

> fitmap #3 inMap #2

Fit molecule F5_J398-a-b-c-coot-2.pdb (#3) to map
cryosparc_P70_J776_008_volume_map.mrc (#2) using 14247 atoms  
average map value = 0.0697, steps = 44  
shifted from previous position = 0.00302  
rotated from previous position = 0.00442 degrees  
atoms outside contour = 11056, contour level = 0.11406  
  
Position of F5_J398-a-b-c-coot-2.pdb (#3) relative to
cryosparc_P70_J776_008_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.91951988 -0.02897443 0.39197406 -16.19473512  
-0.02972343 0.98929715 0.14285540 7.58294791  
-0.39191798 -0.14300920 0.90881718 90.62514911  
Axis -0.34260330 0.93947974 -0.00089766  
Axis point 213.98966670 0.00000000 74.24704270  
Rotation angle (degrees) 24.65760691  
Shift along axis 12.59104458  
  

> vop flip #2

Opened cryosparc_P70_J776_008_volume_map.mrc z flip as #4, grid size
300,300,300, pixel 1.02, shown at step 1, values float32  

> fitmap #3 inMap #4

Fit molecule F5_J398-a-b-c-coot-2.pdb (#3) to map
cryosparc_P70_J776_008_volume_map.mrc z flip (#4) using 14247 atoms  
average map value = 0.1845, steps = 200  
shifted from previous position = 13.4  
rotated from previous position = 27.6 degrees  
atoms outside contour = 3938, contour level = 0.11406  
  
Position of F5_J398-a-b-c-coot-2.pdb (#3) relative to
cryosparc_P70_J776_008_volume_map.mrc z flip (#4) coordinates:  
Matrix rotation and translation  
0.99791802 0.01362056 -0.06304054 30.27766207  
-0.01170048 0.99945932 0.03072745 19.39173545  
0.06342498 -0.02992587 0.99753783 18.21130773  
Axis -0.42556129 -0.88731878 -0.17765971  
Axis point -183.63233517 0.00000000 261.37578417  
Rotation angle (degrees) 4.08651778  
Shift along axis -33.32706757  
  

> lighting soft

> lighting full

> lighting soft

> set bgColor white

> set bgColor #ffffff00

> set bgColor gray

> set bgColor #80808000

> volume #4 style surface

> volume #4 level 0.08727

> volume #4 level 0.1016

> volume #4 level 0.106

> volume #4 level 0.1221

> volume #4 style mesh

> show atoms

> color byhetero

> color bychain

> color byhetero

> volume #4 level 0.1132

> volume #4 level 0.09888

> select ~sel & ##selected

Nothing selected  

> select #1/c:658

Nothing selected  

> select #1/D:658

Nothing selected  

> select #2/D:658

Nothing selected  

> select #3/D:658

11 atoms, 10 bonds, 1 residue, 1 model selected  

> color sel red

> select clear

> volume #4 level 0.08012

> volume #4 level 0.1105

> open
> /Users/hrishikeshdas/Downloads/cryosparc_P70_J789_007_volume_map_sharp.mrc

Opened cryosparc_P70_J789_007_volume_map_sharp.mrc as #5, grid size
300,300,300, pixel 1.02, shown at level 0.0525, step 2, values float32  

> hide #!4-5 target m

> show #!2 target m

> hide #!3 target m

> select ~sel & ##selected

Nothing selected  

> show #!1 target m

> hide #!2 target m

> show #!5 target m

> hide #!1 target m

> vop flip #5

Opened cryosparc_P70_J789_007_volume_map_sharp.mrc z flip as #6, grid size
300,300,300, pixel 1.02, shown at step 1, values float32  

> volume #6 level 0.1861

> volume #6 level 0.2177

> volume #6 level 0.2845

> view

> dust

Unknown command: dust  

> hide dust

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide dust #5 size 3

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide dust #6 size 3

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide dust size 3 #6

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide dust size 3

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide dust size 3

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide dust 3

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide dust

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> ui tool show ""Hide Dust""

> surface dust #6 size 4.25

> surface dust #6 size 3.98

> surface dust #6 size 3.34

> surface dust #6 size 3.12

> surface dust #6 size 1.61

> surface dust #6 size 1.65

> surface dust #6 size 1.79

> surface dust #6 size 1.81

> surface dust #6 size 1.92

> show #!3 models

> fitmap #3 inMap #6

Fit molecule F5_J398-a-b-c-coot-2.pdb (#3) to map
cryosparc_P70_J789_007_volume_map_sharp.mrc z flip (#6) using 14247 atoms  
average map value = 0.3002, steps = 68  
shifted from previous position = 0.281  
rotated from previous position = 0.403 degrees  
atoms outside contour = 7732, contour level = 0.28448  
  
Position of F5_J398-a-b-c-coot-2.pdb (#3) relative to
cryosparc_P70_J789_007_volume_map_sharp.mrc z flip (#6) coordinates:  
Matrix rotation and translation  
0.99800334 0.01982428 -0.05996949 29.21625211  
-0.01805840 0.99939136 0.02984637 20.09234886  
0.06052468 -0.02870382 0.99775390 18.40245480  
Axis -0.42056030 -0.86549782 -0.27210761  
Axis point -138.88910089 0.00000000 248.57023415  
Rotation angle (degrees) 3.99157283  
Shift along axis -34.68452807  
  

> volume #6 style mesh

> volume #6 level 0.2448

> volume #6 style surface

> volume #6 level 0.2117

> surface dust #6 size 1.85

> surface dust #6 size 1.72

> volume #6 level 0.1786

> volume #6 level 0.2084

> volume #6 level 0.2415

> volume #6 level 0.1786

> surface dust #6 size 1.85

> surface dust #6 size 2.24

> surface dust #6 size 2.27

> surface dust #6 size 4.13

> surface dust #6 size 6.91

> surface dust #6 size 6.83

> view

> surface dust #6 size 8.99

> view

> color bychain

> hide #!3 models

> show #!3 models

> view

> volume #6 color #b2b2b2

> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD5/Structures_FAST5/FAST5-trimer/cryosparc_P70_789_007_volume_map_sharp.mrc
> models #6

> close #6

> close

> open
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FASTKD2_paper.cxs
> format session

Opened cryosparc_P43_J469_008_volume_map.mrc as #2, grid size 288,288,288,
pixel 0.902, shown at level 0.0497, step 1, values float32  
Opened cryosparc_P43_J469_008_volume_map_sharp.mrc as #3, grid size
288,288,288, pixel 0.902, shown at level 0.171, step 1, values float32  

> set bgColor #ffffff00

opened ChimeraX session  

> open
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/Stucture/FAST42apo_dimer/F2_coot1-P43_J469-coot-1.pdb

Chain information for F2_coot1-P43_J469-coot-1.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> show #!1 models

> hide #!1 models

> hide #!2 models

> select #1/A

4349 atoms, 4435 bonds, 540 residues, 1 model selected  

> select #4/B

4281 atoms, 4364 bonds, 1 pseudobond, 531 residues, 2 models selected  

> hide sel cartoons

> show #!2 models

> select #4/A

4349 atoms, 4435 bonds, 540 residues, 1 model selected  

> ui tool show ""Color Actions""

> hide #!2 models

> select add #2

4349 atoms, 4435 bonds, 540 residues, 3 models selected  

> show #!1 models

> hide #!1 models

> select add #4

8630 atoms, 8799 bonds, 1 pseudobond, 1071 residues, 4 models selected  

> select subtract #4

2 models selected  

> select subtract #2

Nothing selected  

> show #!1 models

> hide #1.1 models

> hide #!4 models

> show #!4 models

> color #4 #48d6d2ff

> hide #!1 models

> 4/a:457-527

Unknown command: 4/a:457-527  

> select #4/a:457-527

572 atoms, 585 bonds, 71 residues, 1 model selected  

> select #4/a:453-527

605 atoms, 618 bonds, 75 residues, 1 model selected  

> select #4/a:453-549

780 atoms, 795 bonds, 97 residues, 1 model selected  

> Sel #4/a:572-618

Unknown command: Sel #4/a:572-618  

> select #4/a:572-618

375 atoms, 383 bonds, 47 residues, 1 model selected  

> select #1/a:576-695

948 atoms, 967 bonds, 120 residues, 1 model selected  

> select #4/a:576-695

948 atoms, 967 bonds, 120 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel #ef8a62ff

> graphics silhouettes false

> graphics silhouettes true

> select clear

> select #4/a:453-549

780 atoms, 795 bonds, 97 residues, 1 model selected  

> color sel #2166acff

> select clear

> select #4/a:572-618

375 atoms, 383 bonds, 47 residues, 1 model selected  

> select #4/a:457–527

Expected an objects specifier or a keyword  

> select #4/a:457–527

Expected an objects specifier or a keyword  

> select #4/a:457-527

572 atoms, 585 bonds, 71 residues, 1 model selected  

> select clear

> select #4/a:447-307

Nothing selected  

> select #4/a:307-407

808 atoms, 819 bonds, 101 residues, 1 model selected  

> color sel #d1e5f0ff

> color sel #d1e5f0a8

> color sel #d1e5f0a7

> color sel #d1e5f0a8

> select clear

> color #4 #67a9cfa8

> undo

> select #4/a:307-407

808 atoms, 819 bonds, 101 residues, 1 model selected  

> select clear

> select #4/a:307-407

808 atoms, 819 bonds, 101 residues, 1 model selected  

> color #4 #67a9cfff

> undo

> select #4/a:307-407

808 atoms, 819 bonds, 101 residues, 1 model selected  

> color #4 #67a9cfff

> select clear

> undo

> select clear

> select #4/a:307-407

808 atoms, 819 bonds, 101 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel #67a9cfff

> select clear

> color #4 #b2d6d2ff

> color #4 #b2b2d2ff

> color #4 #b2b2b2ff

> select #4/a:307-407

808 atoms, 819 bonds, 101 residues, 1 model selected  

> color #4 #67a9cfff

> select #4/a:307-407

808 atoms, 819 bonds, 101 residues, 1 model selected  

> color sel #02a9cfff

> select clear

> color #4 gray

> color #4 dim gray

> lighting soft

> lighting simple

> color #4 red

> color #4 dim gray

> color #4 light gray

> lighting soft

> select clear

> select #4/a:636-692

453 atoms, 462 bonds, 57 residues, 1 model selected  

> select #4/a:576-692

921 atoms, 939 bonds, 117 residues, 1 model selected  

> color sel #ef8a62ff

> select #4/a:572-618

375 atoms, 383 bonds, 47 residues, 1 model selected  

> select #4/a:457-527

572 atoms, 585 bonds, 71 residues, 1 model selected  

> open
> /Users/hrishikeshdas/Downloads/cryosparc_P70_J815_class_00_00084_volume_sharp.mrc

Opened cryosparc_P70_J815_class_00_00084_volume_sharp.mrc as #5, grid size
128,128,128, pixel 2.03, shown at level 0.0975, step 1, values float32  

> volume #5 level 0.2989

> volume #5 level 0.45

> hide #!4 models

> volume #5 level 0.537

> close #5

> show #!4 models

> select #4/a:572-618

375 atoms, 383 bonds, 47 residues, 1 model selected  

> 636-692

Unknown command: 636-692  

> select #4/a:572-618,636-692

828 atoms, 845 bonds, 104 residues, 1 model selected  

> select #4/a:457–527

Expected an objects specifier or a keyword  

> select #4/a:457-527

572 atoms, 585 bonds, 71 residues, 1 model selected  

> color sel #2166acff

> select #4/a:572-618

375 atoms, 383 bonds, 47 residues, 1 model selected  

> color sel #d1e5f0ff

> select clear

> color #4 #57e5f0ff

> select #4/a:572-618

375 atoms, 383 bonds, 47 residues, 1 model selected  

> color cornflower blue

> undo

> select #4/a:572-618

375 atoms, 383 bonds, 47 residues, 1 model selected  

> color sel cornflower blue

> select clear

> select #4/a:457-531

601 atoms, 614 bonds, 75 residues, 1 model selected  

> color sel #57e5f0ff

> color sel #2166acff

> select clear

> select #4/a:636-692

453 atoms, 462 bonds, 57 residues, 1 model selected  

> select #4/a:636-695

480 atoms, 490 bonds, 60 residues, 1 model selected  

> color sel #ef8a62ff

> select clear

> select #4/a:453-531

634 atoms, 647 bonds, 79 residues, 1 model selected  

> color sel #2166acff

> select clear

> select #4/a:572-618

375 atoms, 383 bonds, 47 residues, 1 model selected  

> select #4/a:636-695

480 atoms, 490 bonds, 60 residues, 1 model selected  

> color sel light gray

> select clear

> select #4/a:636-695

480 atoms, 490 bonds, 60 residues, 1 model selected  

> select #4/a:619-695

604 atoms, 615 bonds, 77 residues, 1 model selected  

> color sel light gray

> select clear

> select #4/a:636-695

480 atoms, 490 bonds, 60 residues, 1 model selected  

> color #4 #ef8a62ff

> undo

> color sel #ef8a62ff

> select clear

> view

> save
> ""/Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2-FAST1-2
> and RAP.jpg"" width 1163 height 850 supersample 4

> view

> save
> ""/Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2-FAST1-2
> and RAP-1.jpg"" width 1163 height 890 supersample 4

> view

> save
> ""/Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2-FAST1-2
> and RAP.jpg"" width 1163 height 890 supersample 4

> turn y 180

> save
> ""/Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2-FAST1-2
> and RAP-1.jpg"" width 1163 height 890 supersample 4

> open /Users/hrishikeshdas/Downloads/cryosparc_P70_J817_012_volume_map.mrc

Opened cryosparc_P70_J817_012_volume_map.mrc as #5, grid size 256,256,256,
pixel 1.02, shown at level 0.0212, step 1, values float32  

> volume #5 level 0.1332

> hide #!4 models

> view

> volume #5 level 0.2064

> volume #5 level 0.235

> select add #5

2 models selected  

> close #5

> show #!4 models

> view

> coulombic #!4

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for F2_coot1-P43_J469-coot-1.pdb_A SES surface #4.2: minimum,
-17.17, mean -0.89, maximum 15.16  
Coulombic values for F2_coot1-P43_J469-coot-1.pdb_B SES surface #4.3: minimum,
-17.76, mean -0.82, maximum 17.84  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide #!4 surfaces

> select #1/B

4281 atoms, 4364 bonds, 1 pseudobond, 531 residues, 2 models selected  

> hide #!4 surfaces

> show #!4 surfaces

> select #1/B

4281 atoms, 4364 bonds, 1 pseudobond, 531 residues, 2 models selected  

> select #1/A#4/A

8698 atoms, 8870 bonds, 1080 residues, 2 models selected  

> hide sel & #!4 surfaces

> hide sel & #!4 cartoons

> hide sel & #!4 surfaces

> select clear

> hide #!4 surfaces

> show #!4 cartoons

> select #4/a:453-531

634 atoms, 647 bonds, 79 residues, 1 model selected  

> select #4/b:453-531

634 atoms, 647 bonds, 79 residues, 1 model selected  

> color (#!4 & sel) #2166acff

> select clear

> select #4/a:636-695

480 atoms, 490 bonds, 60 residues, 1 model selected  

> select #4/b:636-695

480 atoms, 490 bonds, 60 residues, 1 model selected  

> color (#!4 & sel) #d1e5f0ff

> select clear

> select #4/b:636-695

480 atoms, 490 bonds, 60 residues, 1 model selected  

> color (#!4 & sel) #67a9cfff

> select clear

> select ~sel & ##selected

Nothing selected  

> select #4/a:636-695

480 atoms, 490 bonds, 60 residues, 1 model selected  

> select #4/b:636-695

480 atoms, 490 bonds, 60 residues, 1 model selected  

> select #4/a:636-695

480 atoms, 490 bonds, 60 residues, 1 model selected  

> select #4/a:453-531

634 atoms, 647 bonds, 79 residues, 1 model selected  

> select #4/a:572-618

375 atoms, 383 bonds, 47 residues, 1 model selected  

> select clear

> view

> dssp

Computing secondary structure  

> select clear

> select #4/A:631

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #4/A:632

17 atoms, 15 bonds, 2 residues, 2 models selected  

> select add #4/A:633

28 atoms, 25 bonds, 3 residues, 2 models selected  

> select add #4/A:634

35 atoms, 31 bonds, 4 residues, 2 models selected  

> select add #4/A:635

40 atoms, 35 bonds, 5 residues, 2 models selected  

> color (#!4 & sel) #de825bff

> select clear

> select #4/a:453-530

628 atoms, 641 bonds, 78 residues, 1 model selected  

> select #4/a:453-531

634 atoms, 647 bonds, 79 residues, 1 model selected  

> select #4/b:453-531

634 atoms, 647 bonds, 79 residues, 1 model selected  

> select clear

> Sel #4/a:572-618

Unknown command: Sel #4/a:572-618  

> select #4/a:572-618

375 atoms, 383 bonds, 47 residues, 1 model selected  

> select #4/b:572-618

369 atoms, 377 bonds, 46 residues, 1 model selected  

> color (#!4 & sel) #d1e5f0ff

> color (#!4 & sel) #67a9cfff

> select #4/a:576-695

948 atoms, 967 bonds, 120 residues, 1 model selected  

> select clear

> select #4/a:576-631

436 atoms, 444 bonds, 56 residues, 1 model selected  

> select #4/a:636-692

453 atoms, 462 bonds, 57 residues, 1 model selected  

> select #4/a:636-693

461 atoms, 470 bonds, 58 residues, 1 model selected  

> select #4/a:631-693

501 atoms, 510 bonds, 63 residues, 1 model selected  

> color (#!4 & sel) #ef8a62ff

> select #4/b:631-693

501 atoms, 510 bonds, 63 residues, 1 model selected  

> color (#!4 & sel) #ef8a62ff

> select clear

> select #4/B:694

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #4/B:695

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select add #4/B:694

19 atoms, 18 bonds, 2 residues, 2 models selected  

> color (#!4 & sel) #ef8a62ff

> select clear

> dssp

Computing secondary structure  

> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/FAST2_domains.cxs

> select #1/A#4/A

8698 atoms, 8870 bonds, 1080 residues, 2 models selected  

> hide sel & #!4 cartoons

> show sel & #!4 cartoons

> select clear

> select #1/B#4/B

8562 atoms, 8728 bonds, 2 pseudobonds, 1062 residues, 4 models selected  

> hide sel & #!4 cartoons

> view sel

No displayed objects specified.  

> view sel

No displayed objects specified.  

> ui tool show ""Model Panel""

> show target m

> hide #!3 models

> hide #!2 models

> hide #!1 models

> select add #4

12911 atoms, 13163 bonds, 2 pseudobonds, 1602 residues, 5 models selected  

> select subtract #4

4281 atoms, 4364 bonds, 1 pseudobond, 531 residues, 4 models selected  

> select add #1

8630 atoms, 8799 bonds, 1 pseudobond, 1071 residues, 2 models selected  

> select subtract #1

Nothing selected  

> view

> save
> ""/Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2-FAST1-2
> and RAP.jpg"" width 493 height 890 supersample 4

> turn y 180

> save
> ""/Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2-FAST1-2
> and RAP-1.jpg"" width 493 height 890 supersample 4

> view

> select ~sel & ##selected

Nothing selected  

> turn y -180

> view

> save
> ""/Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2-FAST1-2
> and RAP.jpg"" width 1163 height 890 supersample 4

> turn y 180

> save
> ""/Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2-FAST1-2
> and RAP-1.jpg"" width 1163 height 890 supersample 4

> select #4/B

4281 atoms, 4364 bonds, 1 pseudobond, 531 residues, 2 models selected  

> show sel cartoons

> select clear

> select add #4

8630 atoms, 8799 bonds, 1 pseudobond, 1071 residues, 2 models selected  

> show sel surfaces

> color zone #4 near #4

> color zone #4 near #4 distance 5

> select clear

> hide #!4 surfaces

> cofr frontCenter

> view

> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2_a.jpg
> width 1163 height 890 supersample 4

> select #4/b:631-693

501 atoms, 510 bonds, 63 residues, 1 model selected  

> select #4/a:576-695

948 atoms, 967 bonds, 120 residues, 1 model selected  

> select #4/b:453-531

634 atoms, 647 bonds, 79 residues, 1 model selected  

> select #4/a:631-693

501 atoms, 510 bonds, 63 residues, 1 model selected  

> select #4/a:572-618

375 atoms, 383 bonds, 47 residues, 1 model selected  

> color (#!4 & sel) cornflower blue

> select #4/b:572-618

369 atoms, 377 bonds, 46 residues, 1 model selected  

> color (#!4 & sel) cornflower blue

> select clear

> select #1/A#4/A

8698 atoms, 8870 bonds, 1080 residues, 2 models selected  

> hide sel & #!4 cartoons

> show sel & #!4 cartoons

> select clear

> view

> select clear

> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2_a.jpg
> width 1163 height 890 supersample 4

> open
> /Users/hrishikeshdas/Downloads/cryosparc_P70_J809_volumes_all_clusters/J809_cluster_000.mrc

Opened J809_cluster_000.mrc as #5, grid size 300,300,300, pixel 1.02, shown at
level 0.0596, step 2, values float32  

> open
> /Users/hrishikeshdas/Downloads/cryosparc_P70_J809_volumes_all_clusters/J809_cluster_001.mrc

Opened J809_cluster_001.mrc as #6, grid size 300,300,300, pixel 1.02, shown at
level 0.0582, step 2, values float32  

> open
> /Users/hrishikeshdas/Downloads/cryosparc_P70_J809_volumes_all_clusters/J809_cluster_002.mrc

Opened J809_cluster_002.mrc as #7, grid size 300,300,300, pixel 1.02, shown at
level 0.0649, step 2, values float32  

> open
> /Users/hrishikeshdas/Downloads/cryosparc_P70_J809_volumes_all_clusters/J809_cluster_003.mrc

Opened J809_cluster_003.mrc as #8, grid size 300,300,300, pixel 1.02, shown at
level 0.0633, step 2, values float32  

> hide #!4 models

> view

> tile

4 models tiled  

> volume #5 level 0.06618

> volume #5 level 0.06

> volume #5 level 0.05

> volume #5 level 0.04

> volume #5 level 0.07

> volume #6 level 0.07

> volume #7 level 0.07

> volume #8 level 0.07

> volume #8 step 1

> volume #8 level 0.08901

> volume #7 level 0.08

> volume #6 level 0.08

> volume #5 level 0.08

> volume #7 step 1

> volume #6 step 1

> volume #5 step 1

> volume #8 level 0.08

> volume #8 level 0.09

> open /Users/hrishikeshdas/Downloads/cryosparc_P70_J829_007_volume_map.mrc

Opened cryosparc_P70_J829_007_volume_map.mrc as #9, grid size 300,300,300,
pixel 1.02, shown at level 0.0408, step 2, values float32  

> volume #9 level 0.1205

> volume #9 step 1

> view

> volume #9 level 0.1291

> lighting soft

> volume #9 level 0.1452

> volume #9 level 0.1893

> volume #9 level 0.1538

> volume #9 level 0.1344

> volume #9 level 0.1237

> volume #9 level 0.1269

> open /Users/hrishikeshdas/Downloads/cryosparc_P70_J830_006_volume_map.mrc

Opened cryosparc_P70_J830_006_volume_map.mrc as #10, grid size 300,300,300,
pixel 1.02, shown at level 0.0408, step 2, values float32  

> volume #10 level 0.1067

> volume #10 step 1

> volume #10 level 0.1219

> volume #10 level 0.1435

> volume #10 level 0.1327

> volume #10 level 0.1716

> volume #10 level 0.1964

> volume #10 level 0.15

> volume #10 level 0.1273

> volume #10 level 0.1186

> open
> /Users/hrishikeshdas/Downloads/cryosparc_P70_J830_006_volume_map_sharp.mrc

Opened cryosparc_P70_J830_006_volume_map_sharp.mrc as #11, grid size
300,300,300, pixel 1.02, shown at level 0.0568, step 2, values float32  

> volume #11 level 0.1375

> volume #11 step 1

> volume #11 level 0.1478

> ui tool show ""Hide Dust""

> surface dust #11 size 2.46

> surface dust #11 size 1.91

> surface dust #11 size 1.85

> surface dust #11 size 2.22

> surface dust #11 size 2.19

> surface dust #11 size 3.05

> surface dust #11 size 3

> surface dust #11 size 2.15

> surface dust #11 size 2.12

> surface dust #11 size 2.42

> surface dust #11 size 2.38

> volume #11 level 0.1811

> volume #11 level 0.1759

> volume #11 level 0.158

> volume #11 level 0.2323

> open /Users/hrishikeshdas/Downloads/cryosparc_P70_J834__localfilter.mrc

Opened cryosparc_P70_J834__localfilter.mrc as #12, grid size 300,300,300,
pixel 1.02, shown at level 0.0288, step 2, values float32  

> volume #12 level 0.09152

> volume #12 step 1

> volume #12 level 0.1165

> volume #12 level 0.1415

> volume #12 level 0.1165

> volume #12 level 0.2916

> open /Users/hrishikeshdas/Downloads/cryosparc_P70_J833__localfilter.mrc

Opened cryosparc_P70_J833__localfilter.mrc as #13, grid size 300,300,300,
pixel 1.02, shown at level 0.0468, step 2, values float32  

> volume #13 level 0.1035

> volume #13 level 0.09125

> volume #12 level 0.154

> volume #10 level 0.1284

> volume #9 level 0.1409

> volume #9 level 0.1258

> lighting soft

> volume #9 level 0.1431

> open /Users/hrishikeshdas/Downloads/cryosparc_P70_J809_cluster_000.mrc

Opened cryosparc_P70_J809_cluster_000.mrc as #14, grid size 300,300,300, pixel
1.02, shown at level 0.0629, step 2, values float32  

> open /Users/hrishikeshdas/Downloads/cryosparc_P70_J809_cluster_001.mrc

Opened cryosparc_P70_J809_cluster_001.mrc as #15, grid size 300,300,300, pixel
1.02, shown at level 0.0599, step 2, values float32  

> hide #!9 models

> tile

2 models tiled  

> volume #14 step 1

> volume #15 step 1

> volume #15 level 0.07876

> volume #14 level 0.0851

> volume #15 level 0.08935

> volume #15 level 0.08

> volume #14 level 0.085

> volume #14 level 0.08

> close #14

> close #13

> close #15

> view

> lighting soft

> volume #10 level 0.1511

> volume #9 level 0.1291

> view

> show #!1 models

> view

> select ~sel & ##selected

Nothing selected  

> turn y -180

> turn y 180

> turn z 180

> turn z -180

> turn x -180

> turn y 180

> turn z 180

> turn z 90

> turn y 90

> turn y 270

> turn z 270

> turn y -270

> turn y 270

> select ~sel & ##selected

Nothing selected  

> turn y 270

> turn y 90

> turn y \- 90

Expected a number or a keyword  

> turn y -90

> turn y 45

> turn y -45

> turn y -80

> turn y 80

> turn y -80

> turn y 30

> turn y -30

> turn z 30

> turn z -30

> turn y -30

> turn y 30

> turn y 45

> turn y -45

> turn y 45

> turn y -45

> turn x -45

> turn x 45

> turn x 4

> turn x 45

> turn x 40

> turn y 40

> turn x 40

> turn x -60

> turn x -67

> turn x -80

> turn x 80

> turn x 90

> turn x -90

> turn x 90

> turn x 270

> select
> #1/a:196,443,492,247,290,287,283,319,320,356,658,601,194,198,281,282,412,447,449,488,532,535

182 atoms, 165 bonds, 22 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> select
> #1/b:194,281,356,412,447,449,488,532,534,196,193,416,415,443,247,287,290,319,356,603,658,535

185 atoms, 170 bonds, 21 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> select clear

> view

> select clear

> hide #!1 atoms

> select #1/a:193,194,196

26 atoms, 24 bonds, 3 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> select #1/b:193,194,196

26 atoms, 24 bonds, 3 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> select clear

> select #1/B:196

6 atoms, 5 bonds, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #107c01 dashes 5 showDist true restrict cross intraModel
> false twoColors true slopColor #008000 intraRes false select true reveal
> true retainCurrent true log true
    
    
    Finding intermodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 F2_coot1-P43_J469-coot-1.pdb
    	4 F2_coot1-P43_J469-coot-1.pdb
    
    6 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    F2_coot1-P43_J469-coot-1.pdb #1/B SER 196 N   F2_coot1-P43_J469-coot-1.pdb #4/A ARG 194 O   no hydrogen  2.431  N/A
    F2_coot1-P43_J469-coot-1.pdb #1/B SER 196 OG  F2_coot1-P43_J469-coot-1.pdb #4/A LYS 193 O   no hydrogen  3.293  N/A
    F2_coot1-P43_J469-coot-1.pdb #1/B SER 196 OG  F2_coot1-P43_J469-coot-1.pdb #4/A ARG 194 O   no hydrogen  3.195  N/A
    F2_coot1-P43_J469-coot-1.pdb #1/B SER 196 OG  F2_coot1-P43_J469-coot-1.pdb #4/B SER 196 OG  no hydrogen  0.000  N/A
    F2_coot1-P43_J469-coot-1.pdb #4/B SER 196 OG  F2_coot1-P43_J469-coot-1.pdb #1/B SER 196 OG  no hydrogen  0.000  N/A
    F2_coot1-P43_J469-coot-1.pdb #4/B LYS 200 N   F2_coot1-P43_J469-coot-1.pdb #1/B SER 196 O   no hydrogen  2.547  N/A
    

  
6 hydrogen bonds found  
1 strict hydrogen bonds found  

> hbonds sel color #107c01 dashes 5 showDist true restrict cross intraModel
> false twoColors true slopColor #008000 intraRes false select true reveal
> true retainCurrent true log true
    
    
    Finding intermodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 F2_coot1-P43_J469-coot-1.pdb
    	4 F2_coot1-P43_J469-coot-1.pdb
    
    2 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    F2_coot1-P43_J469-coot-1.pdb #4/B SER 196 OG  F2_coot1-P43_J469-coot-1.pdb #1/A LYS 193 O  no hydrogen  3.293  N/A
    F2_coot1-P43_J469-coot-1.pdb #4/B SER 196 OG  F2_coot1-P43_J469-coot-1.pdb #1/A ARG 194 O  no hydrogen  3.195  N/A
    

  
2 hydrogen bonds found  
0 strict hydrogen bonds found  

> hide #!13 models

> hide #13.1 models

> show #13.1 models

> select add #13

3 atoms, 8 pseudobonds, 3 residues, 5 models selected  

> color #13 #000b00ff models

> select clear

> select #1/A:194

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select add #1/A:194

11 atoms, 11 bonds, 1 residue, 1 model selected  

> ui tool show Contacts

> contacts sel overlapCutoff -0.3 resSeparation 5 intraMol false
> ignoreHiddenModels true select true showDist true reveal true

8 contacts  

> hide #14.1 models

> close #14

> select clear

> select #1/B:196

6 atoms, 5 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select clear

> select #1/A:194

11 atoms, 10 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select clear

> select #1/A:194@O

1 atom, 1 residue, 1 model selected  

> select add #1/B:196@N

2 atoms, 2 residues, 1 model selected  

> ui tool show Distances

> distance #1/A:194@O #1/B:196@N

Distance between F2_coot1-P43_J469-coot-1.pdb #1/A ARG 194 O and /B SER 196 N:
2.43Å  

> distance style symbol false

> distance style symbol true

> distance style symbol false

> distance style symbol true

> hide #14.1 models

> select clear

> select #1/B:194

11 atoms, 10 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select clear

> select #1/A:196

6 atoms, 5 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select clear

> select #1/B:194@O

1 atom, 1 residue, 1 model selected  

> select add #1/A:196@N

2 atoms, 2 residues, 1 model selected  

> distance #1/B:194@O #1/A:196@N

Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ARG 194 O and /A SER 196 N:
2.45Å  

> select #1/B:195

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> select #1/B:193

9 atoms, 8 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> select #1/b:198,194,196

25 atoms, 22 bonds, 3 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> select clear

> select #1/B:198@OD2

1 atom, 1 residue, 1 model selected  

> select add #1/A:193@NZ

2 atoms, 2 residues, 1 model selected  

> distance #1/B:198@OD2 #1/A:193@NZ

Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ASP 198 OD2 and /A LYS 193
NZ: 3.80Å  

> select #1/b:198,194,196

25 atoms, 22 bonds, 3 residues, 1 model selected  

> show sel cartoons

> select #1/a:193,194,196

26 atoms, 24 bonds, 3 residues, 1 model selected  

> hide sel cartoons

> show sel cartoons

> select clear

> view

> select #1/a:193,194,196

26 atoms, 24 bonds, 3 residues, 1 model selected  

> select #1/b:198,194,196

25 atoms, 22 bonds, 3 residues, 1 model selected  

> select #1/b:198,194,196

25 atoms, 22 bonds, 3 residues, 1 model selected  

> select #1/a:193,194,196

26 atoms, 24 bonds, 3 residues, 1 model selected  

> select #1/b:198,194,196

25 atoms, 22 bonds, 3 residues, 1 model selected  

> select #1/a:193,194,196

26 atoms, 24 bonds, 3 residues, 1 model selected  

> select #1/b:198,194,196 sel #1/a:193,194,196

Expected a keyword  

> select #1/b:198,194,196, sel #1/a:193,194,196

51 atoms, 46 bonds, 3 pseudobonds, 6 residues, 2 models selected  

> select clear

> view

> select #1/b:198,194,196, sel #1/a:193,194,196

51 atoms, 46 bonds, 3 pseudobonds, 6 residues, 2 models selected  

> view sel

> select clear

> view

> select #1/b:198,194,196, sel #1/a:193,194,196

51 atoms, 46 bonds, 3 pseudobonds, 6 residues, 2 models selected  

> ui tool show ""Side View""

> view sel

> view

> view sel

> view

> view sel

> select clear

> open
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/Stucture/fkd2-coot1_real_space_refined_002-coot-2.pdb

Chain information for fkd2-coot1_real_space_refined_002-coot-2.pdb #15  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> matchmaker #15 to #1

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
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 F2_coot1-P43_J469-coot-1.pdb, chain A (#1) with
fkd2-coot1_real_space_refined_002-coot-2.pdb, chain A (#15), sequence
alignment score = 2772.6  
RMSD between 531 pruned atom pairs is 0.151 angstroms; (across all 534 pairs:
0.311)  
  

> hide #!1 models

> select #15/b:198,194,196, sel #1/a:193,194,196

51 atoms, 46 bonds, 6 residues, 2 models selected  

> select #15/b:198,194,196, sel #1/a:193,194,196

51 atoms, 46 bonds, 6 residues, 2 models selected  

> show sel & #!15 atoms

> select #15/b:198,194,196,sel #1/a:193,194,196

51 atoms, 46 bonds, 6 residues, 2 models selected  

> select #15/b:198,194,196 sel #1/a:193,194,196

Expected a keyword  

> select #15/b:198,194,196

25 atoms, 22 bonds, 3 residues, 1 model selected  

> select #1/a:193,194,196

26 atoms, 24 bonds, 3 residues, 1 model selected  

> select #15/b:198,194,196

25 atoms, 22 bonds, 3 residues, 1 model selected  

> select #15/a:193,194,196

26 atoms, 24 bonds, 3 residues, 1 model selected  

> select #15/b:198,194,196,sel #15/a:193,194,196

51 atoms, 46 bonds, 6 residues, 1 model selected  

> show sel atoms

> select #15/b:198,194,196,sel #15/a:193,194,196,198

59 atoms, 53 bonds, 7 residues, 1 model selected  

> show sel atoms

> select #15/b:198,194,196,193,sel #15/a:193,194,196,198

68 atoms, 62 bonds, 8 residues, 1 model selected  

> show sel atoms

> close #15

Cell requested for row 12 is out of bounds for table with 16 rows! Resizing
table model.  

> close #13

> show #!1 models

> view

> select #15/b:198,194,196,193,sel #15/a:193,194,196,198

Nothing selected  

> select #15/b:198,194,196,193,sel #15/a:193,194,196,198

Nothing selected  

> select #1/b:198,194,196, sel #1/a:193,194,196,198

59 atoms, 53 bonds, 3 pseudobonds, 7 residues, 2 models selected  

> view sel

> view

> view sel

> view

> view sel

> select ~sel & ##selected

8571 atoms, 8746 bonds, 1 pseudobond, 1064 residues, 2 models selected  

> select up

8583 atoms, 8746 bonds, 1 pseudobond, 1071 residues, 2 models selected  

> select up

8630 atoms, 8799 bonds, 1 pseudobond, 1071 residues, 2 models selected  

> select up

8630 atoms, 8799 bonds, 1 pseudobond, 1071 residues, 2 models selected  

> select up

17260 atoms, 17598 bonds, 4 pseudobonds, 2142 residues, 24 models selected  

> select up

17260 atoms, 17598 bonds, 5 pseudobonds, 2142 residues, 27 models selected  

> select up

17260 atoms, 17598 bonds, 5 pseudobonds, 2142 residues, 27 models selected  

> select up

17260 atoms, 17598 bonds, 5 pseudobonds, 2142 residues, 27 models selected  

> select up

17260 atoms, 17598 bonds, 5 pseudobonds, 2142 residues, 27 models selected  

> select up

17260 atoms, 17598 bonds, 5 pseudobonds, 2142 residues, 27 models selected  

> select up

17260 atoms, 17598 bonds, 5 pseudobonds, 2142 residues, 27 models selected  

> select up

17260 atoms, 17598 bonds, 5 pseudobonds, 2142 residues, 27 models selected  

> select up

17260 atoms, 17598 bonds, 5 pseudobonds, 2142 residues, 27 models selected  

> select up

17260 atoms, 17598 bonds, 5 pseudobonds, 2142 residues, 27 models selected  

> select up

17260 atoms, 17598 bonds, 5 pseudobonds, 2142 residues, 27 models selected  

> select up

17260 atoms, 17598 bonds, 5 pseudobonds, 2142 residues, 27 models selected  

> select up

17260 atoms, 17598 bonds, 5 pseudobonds, 2142 residues, 27 models selected  

> select up

17260 atoms, 17598 bonds, 5 pseudobonds, 2142 residues, 27 models selected  

> select clear

> turn x 90

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> turn x -90

> view

> turn x -90

> turn x 90

> turn x -90

> select #1/b:198,194,196, sel #1/a:193,194,196,198

59 atoms, 53 bonds, 3 pseudobonds, 7 residues, 2 models selected  

> view sel

> select clear

> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/interface-4-a.jpg
> width 1163 height 890 supersample 4

> select #1/b:198,194,196, sel #1/a:193,194,196,198

59 atoms, 53 bonds, 3 pseudobonds, 7 residues, 2 models selected  

> hide sel atoms

> color #14 #950000ff models

> color #14 #700000ff models

> color #14 #c00000ff models

> color #14 #c0b100ff models

> color #14 #c0db00ff models

> color #14 #c0fe00ff models

> color #14 #2ffe00ff models

> color #14 #19fe00ff models

> color #14 #0afe00ff models

> select clear

> color #14 #f543e2ff models

> color #14 #ae11f5ff models

> color #14 #9417f5ff models

> select #1/b:198,194,196, sel #1/a:193,194,196,198

59 atoms, 53 bonds, 3 pseudobonds, 7 residues, 2 models selected  

> show sel atoms

> select clear

> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/interface-4-b.jpg
> width 1163 height 890 supersample 4

> select #1/b:198,194,196, sel #1/a:193,194,196,198

59 atoms, 53 bonds, 3 pseudobonds, 7 residues, 2 models selected  

> hide sel atoms

> hide #!14 models

> select add #14

59 atoms, 53 bonds, 3 pseudobonds, 7 residues, 3 models selected  

> select subtract #14

59 atoms, 53 bonds, 7 residues, 1 model selected  

> select clear

> view

> select #1/a:443,492,412,447,449,488

47 atoms, 41 bonds, 6 residues, 1 model selected  

> show sel atoms

> select clear

> select #1/a:443,492,412,447,449,488,319

56 atoms, 49 bonds, 7 residues, 1 model selected  

> select #1/b:247

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> select #1/b:247

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/a:247

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide sel atoms

> select clear

> select #1/a:356

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/b:194,281,356,247,287,290,315

66 atoms, 60 bonds, 7 residues, 1 model selected  

> show sel atoms

> select #1/b:281,356,247,287,290,315

55 atoms, 50 bonds, 6 residues, 1 model selected  

> select #1/B:194

11 atoms, 10 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> hide #!1 models

> select add #5

2 models selected  

> select add #6

4 models selected  

> select add #7

6 models selected  

> view sel

> show #!5 models

> show #!6 models

> show #!7 models

> show #!8 models

> select clear

> hide #!8 models

> show #!3 models

> hide #!3 models

> hide #!7 models

> hide #!6 models

> hide #!5 models

> show #!9 models

> view

> volume #9 level 0.1388

> volume #9 level 0.1291

> open
> /Users/hrishikeshdas/Downloads/cryosparc_P70_J789_007_volume_map_sharp.mrc

Opened cryosparc_P70_J789_007_volume_map_sharp.mrc as #13, grid size
300,300,300, pixel 1.02, shown at level 0.0525, step 2, values float32  

> volume #13 level 0.1758

> volume #13 step 1

> volume #13 level 0.2048

> ui tool show ""Hide Dust""

> surface dust #13 size 1.91

> surface dust #13 size 2.01

> surface dust #13 size 2.72

> volume #13 level 0.1

> volume #13 level 0.04

> volume #13 level 0.09

> volume #13 level 0.1

> volume #13 level 0.2

> volume #13 level 0.3

> volume #13 level 0.25

> set bgColor white

> hide #!13 models

> show #!13 models

> show #!9 models

> hide #!13 models

> view

> hide #!9 models

> show #!14 models

> hide #!14 models

> show #!13 models

> show #!9 models

> hide #!13 models

> volume #9 level 0.1183

> hide #!9 models

> show #!13 models

> hide #!13 models

> show #!13 models

> volume #13 level 0.221

> open
> /Users/hrishikeshdas/Downloads/cryosparc_P70_J880_009_volume_map_sharp.mrc

Opened cryosparc_P70_J880_009_volume_map_sharp.mrc as #15, grid size
300,300,300, pixel 1.02, shown at level 0.0511, step 2, values float32  

> volume #15 level 0.1518

> volume #15 step 1

> volume #15 level 0.2062

> volume #15 level 0.2533

> surface dust #15 size 6.09

> view

> show #!3 models

> hide #!3 models

> show #!4 models

> show #!3 models

> hide #!3 models

> hide #!2 models

> hide #!4 models

> show #!1 models

> hide #!1 atoms

> select #1/b:488,449

13 atoms, 11 bonds, 2 residues, 1 model selected  

> show sel atoms

> select #1/b:488,449,447,412,356,320,319,283,290,287,247

89 atoms, 80 bonds, 11 residues, 1 model selected  

> select #1/b:488,449,447,412,356,320,319,283,290,287,247,492

96 atoms, 86 bonds, 12 residues, 1 model selected  

> select #1/b:488,449,447,412,356,320,319,283,290,287,247,492,443

107 atoms, 96 bonds, 13 residues, 1 model selected  

> show sel atoms

> select clear

> select #1/b:488,449,447,412,356,320,319,283,290,287,247,492,443

107 atoms, 96 bonds, 13 residues, 1 model selected  

> color sel byhetero

> select clear

> select #1/a:281,356,412,447,449,488,416,415,443,247,287,290,283,319

121 atoms, 110 bonds, 14 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> select clear

> select #1/a:281,356,412,447,449,488,416,415,443,247,287,290,283,319

121 atoms, 110 bonds, 14 residues, 1 model selected  

> select #1/a:281,356,412,447,449,488,416,415,443,247,287,290,283,319 sel
> #1/b:488,449,447,412,356,320,319,283,290,287,247,492,443

Expected a keyword  

> select #1/a:281,356,412,447,449,488,416,415,443,247,287,290,283,319, sel
> #1/b:488,449,447,412,356,320,319,283,290,287,247,492,443

228 atoms, 206 bonds, 27 residues, 1 model selected  

> ui tool show Contacts

> contacts sel restrict both overlapCutoff -0.3 resSeparation 5 intraMol false
> ignoreHiddenModels true select true showDist true reveal true

34 contacts  

> show #!15 models

> hide #!15 models

> show #14.1 models

> hide #14.1 models

> hide #!14 models

> hide #4.1 models

> show #4.1 models

> hide #4.1 models

> show #4.1 models

> hide #4.1 models

> hide #!4 models

> hide #4.2 models

> hide #4.3 models

> select add #1

8630 atoms, 8799 bonds, 38 pseudobonds, 1071 residues, 5 models selected  

> select subtract #1

Nothing selected  

> hide #!1.2 models

> show #!1.2 models

> hide #1.2.1 models

> close #1.2

> hide #1.1 models

> show #1.1 models

> hide #!1 models

> show #!1 models

> hide #!3 models

> select #1/a:281,356,412,447,449,488,416,415,443,247,287,290,283,319, sel
> #1/b:488,449,447,412,356,320,319,283,290,287,247,492,443

228 atoms, 206 bonds, 27 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #107c01 dashes 5 showDist true restrict both intraModel
> false twoColors true slopColor #008000 intraRes false select true reveal
> true retainCurrent true log true
    
    
    Finding intermodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 F2_coot1-P43_J469-coot-1.pdb
    
    0 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    

  
0 hydrogen bonds found  
0 strict hydrogen bonds found  

> hide #1.2 models

> show #1.2 models

> select subtract #1.2

Nothing selected  

> select add #1.2

Nothing selected  

> select #1/a:281,356,412,447,449,488,416,415,443,247,287,290,283,319, sel
> #1/b:488,449,447,412,356,320,319,283,290,287,247,492,443

228 atoms, 206 bonds, 27 residues, 1 model selected  

> ui tool show Distances

> ui tool show H-Bonds

> hbonds sel color #107c01 dashes 5 showDist true restrict both intraModel
> false twoColors true slopColor #008000 intraRes false select true reveal
> true retainCurrent true log true
    
    
    Finding intermodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 F2_coot1-P43_J469-coot-1.pdb
    
    0 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    

  
0 hydrogen bonds found  
0 strict hydrogen bonds found  

> hbonds sel color #107c01 dashes 5 showDist true restrict both intraModel
> false twoColors true slopColor #008000 intraRes false select true reveal
> true retainCurrent true log true

Atom specifier selects no atoms  

> select #1/A:412@OD2

1 atom, 1 residue, 1 model selected  

> select #1/B:247@ND2

1 atom, 1 residue, 1 model selected  

> select add #1/A:412@OD2

2 atoms, 2 residues, 1 model selected  

> distance #1/B:247@ND2 #1/A:412@OD2

Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ASN 247 ND2 and /A ASP 412
OD2: 2.65Å  

> show #!14 models

> select clear

> select #1/B:281

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> select #1/A:415@NZ

1 atom, 1 residue, 1 model selected  

> select add #1/B:281@OE2

2 atoms, 2 residues, 1 model selected  

> distance #1/A:415@NZ #1/B:281@OE2

Distance between F2_coot1-P43_J469-coot-1.pdb #1/A LYS 415 NZ and /B GLU 281
OE2: 3.35Å  

> select clear

> select #1/B:281@OE1

1 atom, 1 residue, 1 model selected  

> select add #1/A:443@NH1

2 atoms, 2 residues, 1 model selected  

> distance #1/B:281@OE1 #1/A:443@NH1

Distance between F2_coot1-P43_J469-coot-1.pdb #1/B GLU 281 OE1 and /A ARG 443
NH1: 6.43Å  

> select #1/B:290@NH1

1 atom, 1 residue, 1 model selected  

> select add #1/A:447@OD1

2 atoms, 2 residues, 1 model selected  

> distance #1/B:290@NH1 #1/A:447@OD1

Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ARG 290 NH1 and /A ASP 447
OD1: 3.71Å  

> select clear

> select #1/B:319@NZ

1 atom, 1 residue, 1 model selected  

> select add #1/A:449@OE2

2 atoms, 2 residues, 1 model selected  

> distance #1/B:319@NZ #1/A:449@OE2

Distance between F2_coot1-P43_J469-coot-1.pdb #1/B LYS 319 NZ and /A GLU 449
OE2: 5.49Å  

> select clear

> select #1/A:449@OE2

1 atom, 1 residue, 1 model selected  

> select #1/B:320

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #1/A:449@OE2

9 atoms, 7 bonds, 2 residues, 1 model selected  
Exactly two atoms must be selected!  

> select clear

> select #1/B:320

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select clear

> select #1/B:320@N

1 atom, 1 residue, 1 model selected  

> select add #1/A:449@OE2

2 atoms, 2 residues, 1 model selected  

> distance #1/B:320@N #1/A:449@OE2

Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ASP 320 N and /A GLU 449
OE2: 3.62Å  

> select clear

> show sel cartoons

> select clear

> select #1/B:287

10 atoms, 10 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select clear

> select #1/B:287@ND1

1 atom, 1 residue, 1 model selected  

> select add #1/B:320@OD1

2 atoms, 2 residues, 1 model selected  

> distance #1/B:287@ND1 #1/B:320@OD1

Distance between F2_coot1-P43_J469-coot-1.pdb #1/B HIS 287 ND1 and ASP 320
OD1: 6.32Å  

> select #1/B:287@CA

1 atom, 1 residue, 1 model selected  

> show sel cartoons

> select clear

> select #1/A:492

7 atoms, 6 bonds, 1 residue, 1 model selected  

> show sel atoms

> color sel byhetero

> select clear

> select #1/A:492@OG1

1 atom, 1 residue, 1 model selected  

> select clear

> select #1/B:356@OD1

1 atom, 1 residue, 1 model selected  

> select add #1/A:305

10 atoms, 8 bonds, 2 residues, 1 model selected  

> select clear

> select #1/A:492@OG1

1 atom, 1 residue, 1 model selected  

> select add #1/B:356@OD1

2 atoms, 2 residues, 1 model selected  

> distance #1/A:492@OG1 #1/B:356@OD1

Distance between F2_coot1-P43_J469-coot-1.pdb #1/A THR 492 OG1 and /B ASN 356
OD1: 4.30Å  

> select clear

Drag select of 13 residues, 2 pseudobonds  

> select clear

> select #1/B:283

6 atoms, 5 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select
> #1/a:281,356,412,447,449,488,416,415,443,247,287,290,283,319,492,532,290

136 atoms, 123 bonds, 16 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> select clear

> select #1/A:416@CG

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> select #1/A:416

11 atoms, 11 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> select #1/A:488

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #1/A:488

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select clear

> select #1/A:488

4 atoms, 3 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select clear

> select #1/A:415@CE

1 atom, 1 residue, 1 model selected  

> select clear

> select #1/A:488@O

1 atom, 1 residue, 1 model selected  

> select add #1/B:356@ND2

2 atoms, 2 residues, 1 model selected  

> distance #1/A:488@O #1/B:356@ND2

Distance between F2_coot1-P43_J469-coot-1.pdb #1/A GLY 488 O and /B ASN 356
ND2: 3.58Å  

> select clear

> show sel cartoons

> select clear

> select #1/B:412@OD2

1 atom, 1 residue, 1 model selected  

> select add #1/A:247@ND2

2 atoms, 2 residues, 1 model selected  

> distance #1/B:412@OD2 #1/A:247@ND2

Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ASP 412 OD2 and /A ASN 247
ND2: 3.51Å  

> select #1/A:281@OE2

1 atom, 1 residue, 1 model selected  

> select add #1/B:443@NH1

2 atoms, 2 residues, 1 model selected  

> distance #1/A:281@OE2 #1/B:443@NH1

Distance between F2_coot1-P43_J469-coot-1.pdb #1/A GLU 281 OE2 and /B ARG 443
NH1: 3.24Å  

> select #1/B:287

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select clear

> select add #1/B:412@OD1

1 atom, 1 residue, 1 model selected  

> select add #1/A:281@OE2

2 atoms, 2 residues, 1 model selected  

> distance #1/B:412@OD1 #1/A:281@OE2

Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ASP 412 OD1 and /A GLU 281
OE2: 6.46Å  

> select #1/A:283

6 atoms, 5 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> hide sel atoms

> show sel cartoons

> select clear

> select #1/A:290@NH1

1 atom, 1 residue, 1 model selected  

> select #1/B:379

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select clear

> select #1/A:290@NH1

1 atom, 1 residue, 1 model selected  

> select add #1/B:447@OD2

2 atoms, 2 residues, 1 model selected  

> distance #1/A:290@NH1 #1/B:447@OD2

Distance between F2_coot1-P43_J469-coot-1.pdb #1/A ARG 290 NH1 and /B ASP 447
OD2: 3.70Å  

> select clear

> select #1/B:447@OD1

1 atom, 1 residue, 1 model selected  

> select add #1/A:287@ND1

2 atoms, 2 residues, 1 model selected  

> distance #1/B:447@OD1 #1/A:287@ND1

Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ASP 447 OD1 and /A HIS 287
ND1: 3.10Å  

> select clear

> select #1/A:319@NZ

1 atom, 1 residue, 1 model selected  

> select add #1/B:449@OE2

2 atoms, 2 residues, 1 model selected  

> distance #1/A:319@NZ #1/B:449@OE2

Distance between F2_coot1-P43_J469-coot-1.pdb #1/A LYS 319 NZ and /B GLU 449
OE2: 3.22Å  

> select #1/B:492@OG1

1 atom, 1 residue, 1 model selected  

> select add #1/A:356@ND2

2 atoms, 2 residues, 1 model selected  

> distance #1/B:492@OG1 #1/A:356@ND2

Distance between F2_coot1-P43_J469-coot-1.pdb #1/B THR 492 OG1 and /A ASN 356
ND2: 4.51Å  

> select clear

> view

> open
> /Users/hrishikeshdas/Downloads/cryosparc_P70_J882_class_00_00027_volume.mrc

Opened cryosparc_P70_J882_class_00_00027_volume.mrc as #16, grid size
128,128,128, pixel 2.38, shown at level 0.148, step 1, values float32  

> open
> /Users/hrishikeshdas/Downloads/cryosparc_P70_J882_class_01_00027_volume.mrc

Opened cryosparc_P70_J882_class_01_00027_volume.mrc as #17, grid size
128,128,128, pixel 2.38, shown at level 0.122, step 1, values float32  

> open
> /Users/hrishikeshdas/Downloads/cryosparc_P70_J882_class_02_00027_volume.mrc

Opened cryosparc_P70_J882_class_02_00027_volume.mrc as #18, grid size
128,128,128, pixel 2.38, shown at level 0.143, step 1, values float32  

> hide #!1 models

> hide #1.1 models

> hide #1.2 models

> select subtract #1.2

Nothing selected  

> hide #!14 models

> volume #16 level 0.2141

> volume #16 level 0.2

> volume #17 level 0.2

> volume #18 level 0.2

> volume #18 level 0.247

> volume #16 level 0.1

> volume #16 level 0.4

> volume #16 level 0.3

> volume #17 level 0.3

> volume #18 level 0.3

> close #16-18

> show #!1 models

> show #1.1 models

> open /Users/hrishikeshdas/Downloads/cryosparc_P70_J883_volume_map.mrc

Opened cryosparc_P70_J883_volume_map.mrc as #16, grid size 300,300,300, pixel
1.02, shown at level 0.0423, step 2, values float32  

> hide #!1 models

> hide #1.1 models

> select subtract #1.2

Nothing selected  

> volume #16 level 0.1026

> volume #16 step 1

> volume #16 level 0.1255

> close #16

> open /Users/hrishikeshdas/Downloads/cryosparc_P70_J884_volume_map_sharp.mrc

Opened cryosparc_P70_J884_volume_map_sharp.mrc as #16, grid size 300,300,300,
pixel 1.02, shown at level 0.0579, step 2, values float32  

> volume #16 level 0.1072

> volume #16 step 1

> volume #16 level 0.1333

> volume #16 level 0.1997

> close #16

> show #!1 models

> show #1.1 models

> show #1.2 models

> hide #1.2 models

> close #1.2

> show #!14 models

> dssp

Computing secondary structure  

> dssp

Computing secondary structure  

> select #1/B:196

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select add #1/A:196

12 atoms, 10 bonds, 2 residues, 1 model selected  

> hide sel atoms

> hide #!14 models

> show #!14 models

> select clear

> distance style symbol false

> distance style symbol true

> ~distance #1/A:194@O #1/B:196@N

> ~distance #1/B:281@OE1 #1/A:443@NH1

> undo

Undo failed, probably because structures have been modified.  

> ~distance #1/B:198@OD2 #1/A:193@NZ

> ~distance #1/A:488@O #1/B:356@ND2

> ~distance #1/A:492@OG1 #1/B:356@OD1

> ~distance #1/B:247@ND2 #1/A:412@OD2

> ~distance #1/B:290@NH1 #1/A:447@OD1

> ~distance #1/A:319@NZ #1/B:449@OE2

> ~distance #1/B:194@O #1/A:196@N

> ~distance #1/A:281@OE2 #1/B:443@NH1

> ~distance #1/A:415@NZ #1/B:281@OE2

> ~distance #1/B:412@OD1 #1/A:281@OE2

> ~distance #1/B:447@OD1 #1/A:287@ND1

> ~distance #1/A:290@NH1 #1/B:447@OD2

> ~distance #1/B:287@ND1 #1/B:320@OD1

> ~distance #1/B:319@NZ #1/A:449@OE2

> ~distance #1/B:320@N #1/A:449@OE2

> ~distance #1/B:492@OG1 #1/A:356@ND2

> ~distance #1/B:412@OD2 #1/A:247@ND2

> select #1/A:532

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> select #1/a:532,534,603,658,

Expected an objects specifier or a keyword  

> select #1/b:658,601,532,535dssp

25 atoms, 22 bonds, 3 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> select clear

> select #1/a:532,534,603,658,

Expected an objects specifier or a keyword  

> select #1/b:658,601,532,535

34 atoms, 30 bonds, 4 residues, 1 model selected  

> select #1/a:532,534,603,658

35 atoms, 32 bonds, 4 residues, 1 model selected  

> select #1/b:658,601,532,535

34 atoms, 30 bonds, 4 residues, 1 model selected  

> select #1/a:532,534,603,658.

Expected an objects specifier or a keyword  

> select #1/b:658,601,532,535

34 atoms, 30 bonds, 4 residues, 1 model selected  

> select #1/a:532,534,603,658

35 atoms, 32 bonds, 4 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> select clear

> select #1/B:655

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select clear

> select #1/B:658@NZ

1 atom, 1 residue, 1 model selected  

> select add #1/A:532@OD2

2 atoms, 2 residues, 1 model selected  

> distance #1/B:658@NZ #1/A:532@OD2

Distance between F2_coot1-P43_J469-coot-1.pdb #1/B LYS 658 NZ and /A ASP 532
OD2: 2.54Å  

> select #1/A:534@SD

1 atom, 1 residue, 1 model selected  

> select add #1/B:601@ND2

2 atoms, 2 residues, 1 model selected  

> distance #1/A:534@SD #1/B:601@ND2

Distance between F2_coot1-P43_J469-coot-1.pdb #1/A MET 534 SD and /B ASN 601
ND2: 3.05Å  

> select clear

> select #1/A:658@NZ

1 atom, 1 residue, 1 model selected  

> select add #1/B:532@OD2

2 atoms, 2 residues, 1 model selected  

> distance #1/A:658@NZ #1/B:532@OD2

Distance between F2_coot1-P43_J469-coot-1.pdb #1/A LYS 658 NZ and /B ASP 532
OD2: 3.05Å  

> select clear

> select #1/A:603

10 atoms, 10 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select clear

> select #1/B:532@OD2

1 atom, 1 residue, 1 model selected  

> select add #1/A:603@N

2 atoms, 2 residues, 1 model selected  

> distance #1/B:532@OD2 #1/A:603@N

Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ASP 532 OD2 and /A HIS 603
N: 2.91Å  

> select clear

> show #!1 cartoons

> select clear

> hide #14.1 models

> select clear

> select #1/a:532,534,603,658

35 atoms, 32 bonds, 4 residues, 1 model selected  

> select #1/b:658,601,532,535

34 atoms, 30 bonds, 4 residues, 1 model selected  

> select #1/a:532,534,603,658sel #1/b:658,601,532,535

60 atoms, 54 bonds, 3 pseudobonds, 7 residues, 2 models selected  

> view sel

> select #1/A:532

8 atoms, 7 bonds, 1 residue, 1 model selected  

> view

> select #1/A:412@OD2

1 atom, 1 residue, 1 model selected  

> select add #1/B:247@ND2

2 atoms, 2 residues, 1 model selected  

> distance #1/A:412@OD2 #1/B:247@ND2

Distance between F2_coot1-P43_J469-coot-1.pdb #1/A ASP 412 OD2 and /B ASN 247
ND2: 2.65Å  

> select clear

> select #1/B:281@OE2

1 atom, 1 residue, 1 model selected  

> select add #1/A:415@NZ

2 atoms, 2 residues, 1 model selected  

> distance #1/B:281@OE2 #1/A:415@NZ

Distance between F2_coot1-P43_J469-coot-1.pdb #1/B GLU 281 OE2 and /A LYS 415
NZ: 3.35Å  

> select clear

> select #1/A:443@NH1

1 atom, 1 residue, 1 model selected  

> select add #1/B:281@OE1

2 atoms, 2 residues, 1 model selected  

> distance #1/A:443@NH1 #1/B:281@OE1

Distance between F2_coot1-P43_J469-coot-1.pdb #1/A ARG 443 NH1 and /B GLU 281
OE1: 6.43Å  

> select #1/B:356@ND2

1 atom, 1 residue, 1 model selected  

> select add #1/A:492@OG1

2 atoms, 2 residues, 1 model selected  

> distance #1/B:356@ND2 #1/A:492@OG1

Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ASN 356 ND2 and /A THR 492
OG1: 5.67Å  

> select #1/B:319@NZ

1 atom, 1 residue, 1 model selected  

> select add #1/A:449@OE1

2 atoms, 2 residues, 1 model selected  

> distance #1/B:319@NZ #1/A:449@OE1

Distance between F2_coot1-P43_J469-coot-1.pdb #1/B LYS 319 NZ and /A GLU 449
OE1: 5.58Å  

> select clear

> select #1/B:320@CA

1 atom, 1 residue, 1 model selected  

> hide sel cartoons

> hide sel atoms

> show sel atoms

> select #1/B:320@N

1 atom, 1 residue, 1 model selected  

> select add #1/A:449@OE2

2 atoms, 2 residues, 1 model selected  

> distance #1/B:320@N #1/A:449@OE2

Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ASP 320 N and /A GLU 449
OE2: 3.62Å  

> select clear

> show sel cartoons

> select clear

> select add #1/A:447@OD1

1 atom, 1 residue, 1 model selected  

> select add #1/B:320@OD2

2 atoms, 2 residues, 1 model selected  

> select clear

> select #1/B:290@NH1

1 atom, 1 residue, 1 model selected  

> select add #1/A:447@OD1

2 atoms, 2 residues, 1 model selected  

> distance #1/B:290@NH1 #1/A:447@OD1

Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ARG 290 NH1 and /A ASP 447
OD1: 3.71Å  

> select clear

> select #1/B:287

10 atoms, 10 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select clear

> select #1/A:447@OD2

1 atom, 1 residue, 1 model selected  

> select add #1/B:287@N

2 atoms, 2 residues, 1 model selected  

> distance #1/A:447@OD2 #1/B:287@N

Distance between F2_coot1-P43_J469-coot-1.pdb #1/A ASP 447 OD2 and /B HIS 287
N: 4.43Å  

> select clear

> show sel cartoons

> select clear

> select #1/B:412@OD2

1 atom, 1 residue, 1 model selected  

> select add #1/A:247@ND2

2 atoms, 2 residues, 1 model selected  

> distance #1/B:412@OD2 #1/A:247@ND2

Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ASP 412 OD2 and /A ASN 247
ND2: 3.51Å  

> select clear

> select #1/A:281@OE2

1 atom, 1 residue, 1 model selected  

> select add #1/B:443@NH1

2 atoms, 2 residues, 1 model selected  

> distance #1/A:281@OE2 #1/B:443@NH1

Distance between F2_coot1-P43_J469-coot-1.pdb #1/A GLU 281 OE2 and /B ARG 443
NH1: 3.24Å  

> select #1/a:193,194,196

26 atoms, 24 bonds, 3 residues, 1 model selected  

> select #1/b:198,194,196

25 atoms, 22 bonds, 3 residues, 1 model selected  

> select #1/a:193,194,196sel #1/b:198,194,196

45 atoms, 41 bonds, 5 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> select clear

> select #1/A:200

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select clear

> select #1/A:193@NZ

1 atom, 1 residue, 1 model selected  

> select #1/B:198@OD2

1 atom, 1 residue, 1 model selected  

> select add #1/A:193@NZ

2 atoms, 2 residues, 1 model selected  

> distance #1/B:198@OD2 #1/A:193@NZ

Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ASP 198 OD2 and /A LYS 193
NZ: 3.80Å  

> select #1/A:193@CE

1 atom, 1 residue, 1 model selected  

> select clear

> select #1/B:196

6 atoms, 5 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select clear

> select #1/A:194

11 atoms, 10 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select clear

> select #1/B:196@N

1 atom, 1 residue, 1 model selected  

> select add #1/A:194@O

2 atoms, 2 residues, 1 model selected  

> distance #1/B:196@N #1/A:194@O

Distance between F2_coot1-P43_J469-coot-1.pdb #1/B SER 196 N and /A ARG 194 O:
2.43Å  

> select clear

> select #1/B:194

11 atoms, 10 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select clear

> select #1/b:196

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select clear

> select #1/A:194@CA

1 atom, 1 residue, 1 model selected  

> show sel cartoons

> select clear

> hide sel atoms

> select clear

> select #1/A:194

11 atoms, 10 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #1/B:195

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel cartoons

> select clear

> select #1/B:194@CA

1 atom, 1 residue, 1 model selected  

> select #1/B:195

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/B:195

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select clear

> show sel cartoons

> hide sel atoms

> select clear

> show sel cartoons

> hide sel atoms

> select #1/B:194

11 atoms, 10 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #1/A:278

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select clear

> select #1/A:356@ND2

1 atom, 1 residue, 1 model selected  

> select add #1/B:492@OG1

2 atoms, 2 residues, 1 model selected  

> distance #1/A:356@ND2 #1/B:492@OG1

Distance between F2_coot1-P43_J469-coot-1.pdb #1/A ASN 356 ND2 and /B THR 492
OG1: 4.51Å  

> select #1/A:398

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select clear

> select #1/B:242

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/B:449@OE2

1 atom, 1 residue, 1 model selected  

> select clear

> select #1/B:449@OE2

1 atom, 1 residue, 1 model selected  

> select add #1/A:319@NZ

2 atoms, 2 residues, 1 model selected  

> distance #1/B:449@OE2 #1/A:319@NZ

Distance between F2_coot1-P43_J469-coot-1.pdb #1/B GLU 449 OE2 and /A LYS 319
NZ: 3.22Å  

> select clear

> select #1/B:447@OD1

1 atom, 1 residue, 1 model selected  

> select add #1/A:290@NH1

2 atoms, 2 residues, 1 model selected  

> distance #1/B:447@OD1 #1/A:290@NH1

Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ASP 447 OD1 and /A ARG 290
NH1: 3.67Å  

> select clear

> select #1/A:287

10 atoms, 10 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select clear

> select #1/A:287@N

1 atom, 1 residue, 1 model selected  

> select add #1/B:447@OD2

2 atoms, 2 residues, 1 model selected  

> distance #1/A:287@N #1/B:447@OD2

Distance between F2_coot1-P43_J469-coot-1.pdb #1/A HIS 287 N and /B ASP 447
OD2: 4.19Å  

> select clear

> select #1/A:278

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel cartoons

> select clear

> view

> lighting soft

> lighting simple

> lighting full

> preset cartoons/nucleotides cylinders/stubs

Using preset: Cartoons/Nucleotides / Cylinders/Stubs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> select clear

> lighting soft

> dssp

Computing secondary structure  

> show #!2 models

> hide #!1 models

> hide #1.1 models

> show #!1 models

> hide #!2 models

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> hide #!14 models

> show #!14 models

> preset cartoons/nucleotides cylinders/stubs

Using preset: Cartoons/Nucleotides / Cylinders/Stubs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  
Exactly two atoms must be selected!  

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> hide #!1 models

> hide #!14 models

> open
> /Users/hrishikeshdas/Downloads/cryosparc_P70_J889_008_volume_map_sharp.mrc

Opened cryosparc_P70_J889_008_volume_map_sharp.mrc as #16, grid size
300,300,300, pixel 1.02, shown at level 0.0454, step 2, values float32  

> volume #16 level 0.1381

> volume #16 step 1

> volume #16 level 0.2664

> close #16

> show #!1 models

> open
> /Users/hrishikeshdas/Downloads/cryosparc_P70_J879_class_01_00165_volume.mrc

Opened cryosparc_P70_J879_class_01_00165_volume.mrc as #16, grid size
128,128,128, pixel 2.03, shown at level 0.0762, step 1, values float32  

> open
> /Users/hrishikeshdas/Downloads/cryosparc_P70_J879_class_02_00165_volume.mrc

Opened cryosparc_P70_J879_class_02_00165_volume.mrc as #17, grid size
128,128,128, pixel 2.03, shown at level 0.196, step 1, values float32  

> volume #16 level 0.1605

> hide #!1 models

> volume #17 level 0.2287

> close #17

> volume #16 level 0.2073

> volume #16 level 0.3384

> close #16

> show #!1 models

> select #1/a:281,356,412,447,449,488,416,415,443,247,287,290,283,319,492,290

128 atoms, 116 bonds, 15 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> select clear

> select #1/b:488,449,447,412,356,320,319,283,290,287,247,492,443

107 atoms, 96 bonds, 13 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> select clear

> select #1/A:412@OD2

1 atom, 1 residue, 1 model selected  

> select add #1/B:247@ND2

2 atoms, 2 residues, 1 model selected  

> ~distance #1/B:532@OD2 #1/A:603@N

> ~distance #1/A:447@OD2 #1/B:287@N

> ~distance #1/B:290@NH1 #1/A:447@OD1

> ~distance #1/B:281@OE2 #1/A:415@NZ

> ~distance #1/A:412@OD2 #1/B:247@ND2

> ~distance #1/B:198@OD2 #1/A:193@NZ

> ~distance #1/B:447@OD1 #1/A:290@NH1

> ~distance #1/A:356@ND2 #1/B:492@OG1

> ~distance #1/B:356@ND2 #1/A:492@OG1

> ~distance #1/B:449@OE2 #1/A:319@NZ

> ~distance #1/A:287@N #1/B:447@OD2

> ~distance #1/A:281@OE2 #1/B:443@NH1

> ~distance #1/B:320@N #1/A:449@OE2

> ~distance #1/B:196@N #1/A:194@O

> ~distance #1/A:443@NH1 #1/B:281@OE1

> ~distance #1/A:658@NZ #1/B:532@OD2

> ~distance #1/B:658@NZ #1/A:532@OD2

> ~distance #1/A:534@SD #1/B:601@ND2

> ~distance #1/B:412@OD2 #1/A:247@ND2

> ~distance #1/B:319@NZ #1/A:449@OE1

> distance #1/A:412@OD2 #1/B:247@ND2

Distance between F2_coot1-P43_J469-coot-1.pdb #1/A ASP 412 OD2 and /B ASN 247
ND2: 2.65Å  

> select #1/A:447@OD1

1 atom, 1 residue, 1 model selected  

> select add #1/B:290@NH1

2 atoms, 2 residues, 1 model selected  

> distance #1/A:447@OD1 #1/B:290@NH1

Distance between F2_coot1-P43_J469-coot-1.pdb #1/A ASP 447 OD1 and /B ARG 290
NH1: 3.71Å  

> select #1/B:287

10 atoms, 10 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select clear

> select #1/A:447@OD2

1 atom, 1 residue, 1 model selected  
Exactly two atoms must be selected!  

> select #1/B:287@N

1 atom, 1 residue, 1 model selected  

> select clear

> hide #14.1 models

> select #1/B:281

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> select #1/A:415@NZ

1 atom, 1 residue, 1 model selected  

> select #1/B:281@OE2

1 atom, 1 residue, 1 model selected  

> select clear

> select #1/A:415@NZ

1 atom, 1 residue, 1 model selected  

> select add #1/B:281@OE2

2 atoms, 2 residues, 1 model selected  

> distance #1/A:415@NZ #1/B:281@OE2

Distance between F2_coot1-P43_J469-coot-1.pdb #1/A LYS 415 NZ and /B GLU 281
OE2: 3.35Å  

> select clear

> select #1/A:443@NH1

1 atom, 1 residue, 1 model selected  

> select add #1/B:281@OE1

2 atoms, 2 residues, 1 model selected  

> distance #1/A:443@NH1 #1/B:281@OE1

Distance between F2_coot1-P43_J469-coot-1.pdb #1/A ARG 443 NH1 and /B GLU 281
OE1: 6.43Å  

> select clear

> select #1/B:283

6 atoms, 5 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> select #1/B:287@C

1 atom, 1 residue, 1 model selected  

> select #1/B:288

7 atoms, 6 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> show sel cartoons

> hide sel atoms

> select #1/B:287

10 atoms, 10 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> select #1/A:449

9 atoms, 8 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select clear

> select #1/A:252

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select clear

> select #1/A:449@O

1 atom, 1 residue, 1 model selected  

> select #1/A:449@O

1 atom, 1 residue, 1 model selected  

> select #1/A:449@N

1 atom, 1 residue, 1 model selected  

> select add #1/B:320@OD2

2 atoms, 2 residues, 1 model selected  

> select clear

> select #1/A:449@N

1 atom, 1 residue, 1 model selected  

> select clear

> select #1/A:492

7 atoms, 6 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> select #1/b:492

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select clear

> select #1/A:356@ND2

1 atom, 1 residue, 1 model selected  

> select add #1/B:492@OG1

2 atoms, 2 residues, 1 model selected  

> distance #1/A:356@ND2 #1/B:492@OG1

Distance between F2_coot1-P43_J469-coot-1.pdb #1/A ASN 356 ND2 and /B THR 492
OG1: 4.51Å  

> select clear

> select #1/B:449@OE2

1 atom, 1 residue, 1 model selected  

> select #1/A:319@NZ

1 atom, 1 residue, 1 model selected  

> select add #1/B:449@OE2

2 atoms, 2 residues, 1 model selected  

> distance #1/A:319@NZ #1/B:449@OE2

Distance between F2_coot1-P43_J469-coot-1.pdb #1/A LYS 319 NZ and /B GLU 449
OE2: 3.22Å  

> select #1/B:447@OD1

1 atom, 1 residue, 1 model selected  

> select add #1/A:290@NH1

2 atoms, 2 residues, 1 model selected  

> distance #1/B:447@OD1 #1/A:290@NH1

Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ASP 447 OD1 and /A ARG 290
NH1: 3.67Å  

> select clear

> select #1/A:287

10 atoms, 10 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> select #1/B:443@NH1

1 atom, 1 residue, 1 model selected  

> select add #1/A:281@OE2

2 atoms, 2 residues, 1 model selected  

> distance #1/B:443@NH1 #1/A:281@OE2

Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ARG 443 NH1 and /A GLU 281
OE2: 3.24Å  

> select #1/A:247@ND2

1 atom, 1 residue, 1 model selected  

> select add #1/B:412@OD2

2 atoms, 2 residues, 1 model selected  

> distance #1/A:247@ND2 #1/B:412@OD2

Distance between F2_coot1-P43_J469-coot-1.pdb #1/A ASN 247 ND2 and /B ASP 412
OD2: 3.51Å  

> select clear

> select #1/B:412@OD1

1 atom, 1 residue, 1 model selected  

> select clear

> select #1/A:283@CA

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> show sel cartoons

Drag select of 2 residues  

> select clear

> select #1/B:319@NZ

1 atom, 1 residue, 1 model selected  

> select clear

> select #1/B:319

9 atoms, 8 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select clear

> select #1/A:449@OE2

1 atom, 1 residue, 1 model selected  

> select add #1/B:319@N

2 atoms, 2 residues, 1 model selected  

> distance #1/A:449@OE2 #1/B:319@N

Distance between F2_coot1-P43_J469-coot-1.pdb #1/A GLU 449 OE2 and /B LYS 319
N: 3.24Å  

> select clear

> select #1/B:319@N

1 atom, 1 residue, 1 model selected  

> show sel cartoons

> select clear

> select #1/B:320

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select clear

> select #1/B:320@CA

1 atom, 1 residue, 1 model selected  

> show sel cartoons

> hide sel atoms

> select clear

> select add #1/B:320@OD2

1 atom, 3 bonds, 1 residue, 1 model selected  

> select add #1/B:320@CB

2 atoms, 3 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select clear

Drag select of 2 atoms, 1 residues, 1 bonds  

> hide sel atoms

> select clear

> select #1/A:488

4 atoms, 3 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select clear

> select #1/A:488@O

1 atom, 1 residue, 1 model selected  

> select add #1/B:356@ND2

2 atoms, 2 residues, 1 model selected  

> distance #1/A:488@O #1/B:356@ND2

Distance between F2_coot1-P43_J469-coot-1.pdb #1/A GLY 488 O and /B ASN 356
ND2: 3.58Å  

> select clear

> show sel cartoons

> select clear

> select #1/B:247@CA

1 atom, 1 residue, 1 model selected  

> select add #1/A:412

9 atoms, 7 bonds, 2 residues, 1 model selected  

> select add #1/A:443

20 atoms, 17 bonds, 3 residues, 1 model selected  

> select add #1/B:281

29 atoms, 25 bonds, 4 residues, 1 model selected  

> select add #1/A:415

38 atoms, 33 bonds, 5 residues, 1 model selected  

> select add #1/B:290

49 atoms, 43 bonds, 6 residues, 1 model selected  

> select add #1/A:449

58 atoms, 51 bonds, 7 residues, 1 model selected  

> select add #1/B:319

67 atoms, 59 bonds, 8 residues, 1 model selected  

> select add #1/B:356

75 atoms, 66 bonds, 9 residues, 1 model selected  

> select add #1/A:488

79 atoms, 69 bonds, 10 residues, 1 model selected  

> select add #1/A:447

87 atoms, 76 bonds, 11 residues, 1 model selected  

> view sel

> select clear

> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/interface-2a.jpg
> width 2696 height 1890 supersample 4

> select #1/A:416

11 atoms, 11 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/interface-2a.jpg
> width 2696 height 1890 supersample 4

> style #!1 stick

Changed 8630 atom styles  

> hide #!1 models

> show #!1 models

> open /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD1/FASTKD1.pdb

FASTKD1.pdb title:  
Alphafold monomer V2.0 prediction for fast kinase domain-containing protein 1,
mitochondrial (Q53R41) [more info...]  
  
Chain information for FASTKD1.pdb #16  
---  
Chain | Description | UniProt  
A | fast kinase domain-containing protein 1, mitochondrial | FAKD1_HUMAN 1-847  
  
Computing secondary structure  

> hide #!1 models

> view

> rainbow #16

> select clear

> select #16/A:61

5 atoms, 4 bonds, 1 residue, 1 model selected  

> show sel atoms

> close #16

> show #!1 models

> view

> show #1.1 models

> select #1/A:247

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:281

9 atoms, 8 bonds, 1 residue, 1 model selected  

> hide sel atoms

> show sel atoms

> hide sel atoms

> select clear

> select #1/A:283@SG

1 atom, 1 residue, 1 model selected  

> show sel cartoons

> hide sel cartoons

> show sel cartoons

> hide sel atoms

> show sel atoms

> select #1/A:283

6 atoms, 5 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide sel atoms

> select clear

> select #1/A:290

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #1/A:319

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:356

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/B:412

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select clear

> select #1/B:443

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #1/B:447

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select clear

> select #1/B:449

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/B:492

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select clear

> select #1/a:247,281,290,319,356sel #1/b:412,443,447,449,492

80 atoms, 71 bonds, 4 pseudobonds, 9 residues, 2 models selected  

> select #1/A:356

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/a:247,281,290,319,356 sel #1/b:412,443,447,449,492

Expected a keyword  

> select #1/a:247,281,290,319,356, sel #1/b:412,443,447,449,492

88 atoms, 78 bonds, 5 pseudobonds, 10 residues, 2 models selected  

> select clear

> select #1/A:412@CA

1 atom, 1 residue, 1 model selected  

> select clear

> select #1/A:412@CA

1 atom, 1 residue, 1 model selected  

> select #1/A:412

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select clear

> select #1/A:415

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:443

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select clear

> select #1/A:447

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select clear

> select #1/A:447

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select clear

> select #1/A:449

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select clear

> select #1/A:488

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #1/A:488

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select clear

> select #1/B:247

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select clear

> select #1/B:281

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select clear

> select #1/B:290

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select clear

> select #1/B:354

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select clear

> select #1/B:320

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/B:319

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select clear

> select #1/B:356@CA

1 atom, 1 residue, 1 model selected  

> select #1/B:356

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select clear

> select #1/a:412,415,443,447,449,488,sel #1/b:247,281,290,319,356

94 atoms, 83 bonds, 6 pseudobonds, 11 residues, 2 models selected  

> view

> view sel

> view orient

> view

> select up

593 atoms, 598 bonds, 6 pseudobonds, 75 residues, 2 models selected  

> select down

94 atoms, 83 bonds, 6 pseudobonds, 11 residues, 2 models selected  

> turn y 90

> select clear

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> turn y -90

> view

> select #1/a:193,194,196,sel #1/b:198,194,196

51 atoms, 46 bonds, 6 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> select clear

> select #1/A:193@NZ

1 atom, 1 residue, 1 model selected  

> select #1/B:198@OD2

1 atom, 1 residue, 1 model selected  

> select add #1/A:193@NZ

2 atoms, 2 residues, 1 model selected  

> distance #1/B:198@OD2 #1/A:193@NZ

Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ASP 198 OD2 and /A LYS 193
NZ: 3.80Å  

> select clear

> select #1/B:196@CA

1 atom, 1 residue, 1 model selected  

> hide sel cartoons

> select clear

> select #1/B:196@OG

1 atom, 1 residue, 1 model selected  

> hide sel cartoons

> select clear

> select #1/A:194@N

1 atom, 1 residue, 1 model selected  

> select add #1/B:196@OG

2 atoms, 2 residues, 1 model selected  

> distance #1/A:194@N #1/B:196@OG

Distance between F2_coot1-P43_J469-coot-1.pdb #1/A ARG 194 N and /B SER 196
OG: 4.37Å  

> select clear

> show sel cartoons

> select clear

> select #1/B:194

11 atoms, 10 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select clear

> select #1/B:194@O

1 atom, 1 residue, 1 model selected  

> select #1/A:196

6 atoms, 5 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select clear

> select #1/A:196@N

1 atom, 1 residue, 1 model selected  

> select add #1/B:194@O

2 atoms, 2 residues, 1 model selected  

> distance #1/A:196@N #1/B:194@O

Distance between F2_coot1-P43_J469-coot-1.pdb #1/A SER 196 N and /B ARG 194 O:
2.45Å  

> select clear

> show sel cartoons

> select clear

> select #1/B:196@N

1 atom, 1 residue, 1 model selected  

> show sel cartoons

> select clear

> select #1/a:532,534,603,658,sel #1/b:658,601,532,535

69 atoms, 62 bonds, 8 residues, 1 model selected  

> show sel atoms

> select clear

> select #1/B:532@OD2

1 atom, 1 residue, 1 model selected  

> select add #1/A:658@NZ

2 atoms, 2 residues, 1 model selected  

> distance #1/B:532@OD2 #1/A:658@NZ

Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ASP 532 OD2 and /A LYS 658
NZ: 3.05Å  

> select clear

> select #1/A:603@CA

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> select #1/A:603

10 atoms, 10 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> show sel cartoons

> show sel atoms

> hide sel atoms

> select clear

> select #1/A:532@OD2

1 atom, 1 residue, 1 model selected  

> select add #1/B:658@NZ

2 atoms, 2 residues, 1 model selected  

> distance #1/A:532@OD2 #1/B:658@NZ

Distance between F2_coot1-P43_J469-coot-1.pdb #1/A ASP 532 OD2 and /B LYS 658
NZ: 2.54Å  

> select clear

> select add #1/B:601

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #1/A:534

16 atoms, 14 bonds, 2 residues, 1 model selected  

> hide sel atoms

> select clear

> view

> show #!6 models

> hide #!6 models

> close #5-8

> show #!9 models

> hide #!9 models

> close #9-13

> show #!15 models

> hide #!15 models

> close #15

Cell requested for row 3 is out of bounds for table with 10 rows! Resizing
table model.  

> show #!3 models

> hide #!3 models

> show #!2 models

> hide #!2 models

> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2_interactions.cxs

> select #1/B:535

9 atoms, 8 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> select #1/B:194@CA

1 atom, 1 residue, 1 model selected  

> show sel cartoons

> select clear

> select #1/B:194

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #1/A:194

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select clear

> turn y 90

> turn y -90

> select ~sel & ##selected

Nothing selected  

> turn y 90

> turn y -90

> turn y 90

> turn x 90

> turn x -90

> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2_interactions_atoms-1.jpg
> width 2696 height 1890 supersample 4

> select #1/a:193,194,196,sel #1/b:198,194,196

51 atoms, 46 bonds, 3 pseudobonds, 6 residues, 2 models selected  

> turn x 90

> turn x -90

> view sel

> select clear

> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/interface-1a.jpg
> width 2696 height 1890 supersample 4

> turn x 90

> view

> turn x -90

> select #1/B:198

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select clear

> turn x -90

> turn x 90

> select #1/B:532@CA

1 atom, 1 residue, 1 model selected  

> select #1/A:428

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/B:532@CA

1 atom, 1 residue, 1 model selected  

> select clear

> select #1/B:532@CA

1 atom, 1 residue, 1 model selected  

> select #1/B:532@CA

1 atom, 1 residue, 1 model selected  

> select clear

> select #1/a:532,534,603,658,sel #1/b:658,601,532,535

69 atoms, 62 bonds, 2 pseudobonds, 8 residues, 2 models selected  

> select #1/A:534

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:534

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/a:532,534,603,658,sel #1/b:658,601,532,535

69 atoms, 62 bonds, 2 pseudobonds, 8 residues, 2 models selected  

> view sel

> select clear

> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/interface4-a.jpg
> width 2696 height 1890 supersample 4

> turn x -90

> view

> select #1/a:247,281,290,319,356,sel #1/b:412,443,447,449,492

88 atoms, 78 bonds, 5 pseudobonds, 10 residues, 2 models selected  

> select clear

> view

> select #1/a:247,281,290,319,356,sel #1/b:412,443,447,449,492

88 atoms, 78 bonds, 5 pseudobonds, 10 residues, 2 models selected  

> turn y -90

> view sel

> select clear

> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/interface3-a.jpg
> width 2696 height 1890 supersample 4

> view

> select #1/A:247

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/a:247,281,290,319,356,sel #1/b:412,443,447,449,492

88 atoms, 78 bonds, 5 pseudobonds, 10 residues, 2 models selected  

> turn y -90

> view sel

> view

> select clear

> select #1/a:247,281,290,319,356,sel #1/b:412,443,447,449,492

88 atoms, 78 bonds, 5 pseudobonds, 10 residues, 2 models selected  

> select #1/a:412,415,443,447,449,488,sel #1/b:247,281,290,319,356

94 atoms, 83 bonds, 6 pseudobonds, 11 residues, 2 models selected  

> view sel

> view

> turn y 90

> view sel

> select clear

> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/interface2-a.jpg
> width 2696 height 1890 supersample 4

> view

> open /Users/hrishikeshdas/Downloads/cryosparc_P70_J927_006_volume_map.mrc

Opened cryosparc_P70_J927_006_volume_map.mrc as #5, grid size 256,256,256,
pixel 1.02, shown at level 0.0167, step 1, values float32  

> volume #5 level 0.0624

> volume #5 level 0.08581

> hide #!1 models

> hide #1.1 models

> hide #!5 models

> show #!5 models

> hide #!14 models

> volume #5 level 0.1014

> ui tool show ""Hide Dust""

> surface dust #5 size 26.28

> select ~sel & ##selected

Nothing selected  

> volume #5 level 0.11

> vop threshold #5 minimum 0.11 set 0

Opened cryosparc_P70_J927_006_volume_map.mrc thresholded as #6, grid size
256,256,256, pixel 1.02, shown at step 1, values float32  

> surface dust #6 size 9.98

> surface dust #6 size 11.03

> surface dust #6 size 18.51

> vop threshold #6 maximum 0.1 set 1

Opened cryosparc_P70_J927_006_volume_map.mrc thresholded as #7, grid size
256,256,256, pixel 1.02, shown at step 1, values float32  

> volume #7 level 0.08614

> surface dust #6 size 18.51

> surface dust #7 size 6.09

> surface dust #7 size 6.47

> surface dust #7 size 17.03

> surface dust #7 size 16.75

> surface dust #7 size 1.02

> ui tool show ""Map Eraser""

> select add #8

1 model selected  

> ui mousemode right zoom

> ui mousemode right ""translate selected models""

> view matrix models #8,1,0,0,91.777,0,1,0,132.21,0,0,1,128.03

> volume erase #7 center 91.777,132.21,128.03 radius 14.343

> view matrix models #8,1,0,0,98.765,0,1,0,154.52,0,0,1,134.97

> volume erase #7 center 98.765,154.52,134.97 radius 14.343

No map chosen to save  

> save /Users/hrishikeshdas/Desktop/J972_p70_forMask.mrc models #7

> close #7

> close #6

> show #!5 models

> close #5

> close #8

> show #!1 models

> select clear

> turn y 90

> turn y -90

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> turn y 90

> turn x 90


===== 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/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FASTKD2_paper.cxs

Opened cryosparc_P43_J469_008_volume_map.mrc as #2, grid size 288,288,288,
pixel 0.902, shown at level 0.0497, step 1, values float32  
Opened cryosparc_P43_J469_008_volume_map_sharp.mrc as #3, grid size
288,288,288, pixel 0.902, shown at level 0.171, step 1, values float32  
Log from Sun Jan 26 10:09:07 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/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/Stucture/FAST42apo_dimer/F2_coot1-P43_J469-coot-1.pdb

Chain information for F2_coot1-P43_J469-coot-1.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/Stucture/FAST42apo_dimer/cryosparc_P43_J469_008_volume_map.mrc

Opened cryosparc_P43_J469_008_volume_map.mrc as #2, grid size 288,288,288,
pixel 0.902, shown at level 0.00703, step 2, values float32  

> lighting soft

[Repeated 1 time(s)]

> color bypolymer

> volume #2 level 0.03766

> volume #2 step 1

> lighting soft

> set bgColor white

> graphics silhouettes true

> select /A

4349 atoms, 4435 bonds, 540 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel #fbe7c6ff

> graphics silhouettes false

> graphics silhouettes true

> select clear

> select /B

4281 atoms, 4364 bonds, 1 pseudobond, 531 residues, 2 models selected  

> color (#!1 & sel) #a0e7e5ff

> select clear

> dssp

Computing secondary structure  

> volume #2 level 0.03946

> volume #2 level 0.04489

> hide #!2 models

> hide #!1 models

> show #!2 models

> volume #2 level 0.04971

> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FASTKD2_paper.cxs

> show #!1 models

> show #!2 models

> open
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/Stucture/FAST42apo_dimer/cryosparc_P43_J469_008_volume_map_sharp.mrc

Opened cryosparc_P43_J469_008_volume_map_sharp.mrc as #3, grid size
288,288,288, pixel 0.902, shown at level 0.0405, step 2, values float32  

> volume #3 level 0.09217

> volume #3 step 1

> volume #3 level 0.09441

> volume #3 level 0.1191

> volume #3 level 0.1326

> volume #3 level 0.1349

> volume #3 level 0.1506

> volume #3 level 0.1641

> volume #3 level 0.1686

> volume #3 level 0.1708

> hide #!3 models

> show #!3 models

> hide #!3 models

> hide #!1 models

> volume #3 color white

> volume #3 color #b2ffff

> volume #3 color #b2b2ff

> volume #3 color #b2b2b2

> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FASTKD2_paper.cxs

> color #2 near #1 5

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color zone #2 near #1 distance 5

> lighting soft

> lighting full

> lighting simple

> lighting soft

> view

> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FASTKD2_paper.cxs

> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/MAP_surface-1.jpg
> width 1163 height 850 supersample 4

> view

> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/paper_FASTKD2/MAP_surface-1.jpg
> width 1163 height 850 supersample 3

> turn y 90

> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/paper_FASTKD2/MAP_surface-2.jpg
> width 1163 height 850 supersample 3

> turn y 90

> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/paper_FASTKD2/MAP_surface-3.jpg
> width 1163 height 850 supersample 3

> turn z 90

> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/paper_FASTKD2/MAP_surface-4.jpg
> width 1163 height 850 supersample 3

> turn z 90

[Repeated 6 time(s)]

> turn y -90

[Repeated 1 time(s)]

> turn x 90

> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/paper_FASTKD2/MAP_surface-5.jpg
> width 1163 height 850 supersample 3

> select ~sel & ##selected

Nothing selected  

> turn x 180

> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/paper_FASTKD2/MAP_surface-6.jpg
> width 1163 height 850 supersample 3

> turn x -180

> hide #!2 models

> show #!1 models

> select /A

4349 atoms, 4435 bonds, 540 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel #48d6d2ff

> select /A

4349 atoms, 4435 bonds, 540 residues, 1 model selected  

> select /B

4281 atoms, 4364 bonds, 1 pseudobond, 531 residues, 2 models selected  

> color (#!1 & sel) #fefcbfff

> select clear

> dssp

Computing secondary structure  

> select clear

> color zone #2 near #1 distance 4

> show #!2 models

> hide #!1 models

> lighting full

> lighting soft

> show #!1 models

> hide #!2 models

> show #!2 models

> show #!3 models

> hide #!2 models

> hide #!1 models

> color zone #3 near #1 distance 4

> hide #!3 models

> show #!2 models

> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FASTKD2_paper.cxs

> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2_surface.jpg
> width 1163 height 850 supersample 4

> select ~sel & ##selected

Nothing selected  

> turn y 90

> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2_surface_turnY90.jpg
> width 1163 height 850 supersample 4

> turn y 90

> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2_surface_turnY90Y90.jpg
> width 1163 height 850 supersample 4

> turn y 90

> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2_surface_turnY90Y90Y90.jpg
> width 1163 height 850 supersample 4

> turn y 90

> turn x 90

> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2_surface-X90.jpg
> width 1163 height 850 supersample 3

> turn x -90

[Repeated 1 time(s)]

> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2_surfaceX90.jpg
> width 1163 height 850 supersample 3

> turn x 90

> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FASTKD2_paper.cxs

——— End of log from Sun Jan 26 10:09:07 2025 ———

opened ChimeraX session  




OpenGL version: 4.1 ATI-6.1.13
OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: 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: MacBookPro16,1
      Processor Name: 6-Core Intel Core i7
      Processor Speed: 2,6 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 12 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 2069.80.3.0.0 (iBridge: 22.16.13051.0.0,0)
      OS Loader Version: 582~3311

Software:

    System Software Overview:

      System Version: macOS 15.3.1 (24D70)
      Kernel Version: Darwin 24.3.0
      Time since boot: 7 days, 10 hours, 58 minutes

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0000
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3

    AMD Radeon Pro 5300M:

      Chipset Model: AMD Radeon Pro 5300M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0043
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32207P1-019
      Option ROM Version: 113-D32207P1-019
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


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-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-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
    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
}}}
"	defect	new	normal		Unassigned