id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
18674	ChimeraX bug report submission	nuren.tasneem@…		"{{{
The following bug report has been submitted:
Platform:        macOS-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 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 0x00000001f62fa0c0 (most recent call first):
  File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 368 in event_loop
  File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1057 in init
  File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1220 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, chimerax.surface._surface, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imaging, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.mlp._mlp, _pyKVFinder (total: 61)


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===== Log before crash start =====
UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/BIO-
> SAXS_data/AvrStb6_dimer_refine_027.pdb format pdb

Chain information for AvrStb6_dimer_refine_027.pdb #1  
---  
Chain | Description  
A B | No description available  
  
Computing secondary structure  

> lighting soft

> graphics silhouettes true

> select clear

> hide atoms

> select ::name=""CYS""

240 atoms, 230 bonds, 24 residues, 1 model selected  

> show sel atoms

> select clear

> hide #1 models

> open 4fz0

Summary of feedback from opening 4fz0 fetched from pdb  
---  
notes | Fetching compressed mmCIF 4fz0 from http://files.rcsb.org/download/4fz0.cif  
Fetching CCD GOL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/GOL/GOL.cif  
Fetching CCD NAG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NAG/NAG.cif  
  
4fz0 title:  
Crystal structure of acid-sensing ion channel in complex with psalmotoxin 1 at
low pH [more info...]  
  
Chain information for 4fz0 #2  
---  
Chain | Description | UniProt  
A B C | Acid-sensing ion channel 1 | ASIC1_CHICK 14-463  
M N O | Pi-theraphotoxin-Pc1a | TXP1_PSACA 1-40  
  
Non-standard residues in 4fz0 #2  
---  
CL — chloride ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  

> sequence chain #2/A#2/B#2/C

Alignment identifier is 1  

> select #2/M

299 atoms, 304 bonds, 43 residues, 1 model selected  

> select ~sel

12081 atoms, 12180 bonds, 1632 residues, 2 models selected  

> hide sel & #2 cartoons

> hide sel & #2 atoms

> select clear

> show #2 cartoons

> hide #2 atoms

> select #2/M

299 atoms, 304 bonds, 43 residues, 1 model selected  

> select ~sel

12081 atoms, 12180 bonds, 1632 residues, 2 models selected  

> hide sel & #2 cartoons

> select clear

> graphics silhouettes width 1

> lighting soft

> select clear

> select #2/M:2-38

293 atoms, 304 bonds, 37 residues, 1 model selected  
Alignment identifier is 2/M  

> select clear

> select #2/M:3

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

> select #2/M:3

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

> select #2/M:10

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

> select #2/M:10

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

> select #2/M:3,10

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

> select #2/M:3,10,17-18

24 atoms, 22 bonds, 4 residues, 1 model selected  

> select #2/M:3,10,17-18,23

30 atoms, 28 bonds, 5 residues, 1 model selected  

> select #2/M:3,10,17-18,23,33

36 atoms, 34 bonds, 6 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 36 atom styles  

> color sel byhetero

> select clear

> color #2 #76d6ffff

> color #2 #ebebebff

> color #2 #d6d6d6ff

> color #2 #ebebebff

> color #2 #d6d6d6ff

> color #2 #ebebebff

> color #2 #d6d6d6ff

> select #2/M:3

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

> select #2/M:3

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

> select #2/M:3,10

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

> select #2/M:3,10,17-18

24 atoms, 22 bonds, 4 residues, 1 model selected  

> select #2/M:3,10,17-18,23

30 atoms, 28 bonds, 5 residues, 1 model selected  

> select #2/M:3,10,17-18,23,33

36 atoms, 34 bonds, 6 residues, 1 model selected  

> color sel byhetero

> select clear

> save /Users/u6290062/Documents/PhD/Manuscripts/01_Stb6-AvrStb6/Data/4fz0.png
> width 867 height 739 supersample 4 transparentBackground true

> select add #2

10557 atoms, 10686 bonds, 1486 residues, 1 model selected  

> close #2

> show #1 models

> view clip false

> open 8f2f

Summary of feedback from opening 8f2f fetched from pdb  
---  
note | Fetching compressed mmCIF 8f2f from http://files.rcsb.org/download/8f2f.cif  
  
8f2f title:  
NMR solution structure of lambda-MeuKTx-1 [more info...]  
  
Chain information for 8f2f  
---  
Chain | Description | UniProt  
2.1/A 2.2/A 2.3/A 2.4/A 2.5/A 2.6/A 2.7/A 2.8/A 2.9/A 2.10/A 2.11/A 2.12/A 2.13/A 2.14/A 2.15/A 2.16/A 2.17/A 2.18/A 2.19/A 2.20/A | Neurotoxin lambda-MeuTx | CLML_MESEU 1-37  
  

> close #2

Alignment identifier is 1  

> select /B

880 atoms, 896 bonds, 66 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select clear

> select /A:42

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

> select /A:42-71

399 atoms, 407 bonds, 30 residues, 1 model selected  

> select ~sel & ##selected

544 atoms, 495 bonds, 93 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select clear

> save /Users/u6290062/Documents/Figures/AvrStb6-CT.pdb displayedOnly true
> relModel #1

> open 2r33

Summary of feedback from opening 2r33 fetched from pdb  
---  
note | Fetching compressed mmCIF 2r33 from http://files.rcsb.org/download/2r33.cif  
  
2r33 title:  
Crystal structure of a Bowman-Birk inhibitor from Vigna unguiculata seeds
[more info...]  
  
Chain information for 2r33 #2  
---  
Chain | Description  
A B | Bowman-Birk type seed trypsin and chymotrypsin inhibitor  
  

> ui tool show Matchmaker

> matchmaker #!2 to #1

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 AvrStb6_dimer_refine_027.pdb, chain A (#1) with 2r33, chain B (#2),
sequence alignment score = 55.3  
RMSD between 10 pruned atom pairs is 0.426 angstroms; (across all 28 pairs:
6.582)  
  

> select ::name=""CYS""

228 atoms, 213 bonds, 34 residues, 2 models selected  

> show sel atoms

> select clear

> open /Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/BIO-
> SAXS_data/AvrStb6_dimer_refine_027.pdb

Chain information for AvrStb6_dimer_refine_027.pdb #3  
---  
Chain | Description  
A B | No description available  
  
Computing secondary structure  

> select clear

> hide atoms

> ui tool show Matchmaker

> matchmaker #3 to #2

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 2r33, chain A (#2) with AvrStb6_dimer_refine_027.pdb, chain A (#3),
sequence alignment score = 68.5  
RMSD between 9 pruned atom pairs is 0.998 angstroms; (across all 45 pairs:
9.832)  
  

> hide #1 models

> ui tool show Matchmaker

> matchmaker #3 & sel to #2 & sel

No 'to' model specified  

> matchmaker #3 & sel to #2 & sel

No 'to' model specified  

> matchmaker #3 to #2 & sel

No 'to' model specified  

> matchmaker #3 to #2

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 2r33, chain A (#2) with AvrStb6_dimer_refine_027.pdb, chain A (#3),
sequence alignment score = 68.5  
RMSD between 9 pruned atom pairs is 0.998 angstroms; (across all 45 pairs:
9.832)  
  

> select clear

> hide #3 models

> show #1 models

> close

> open /Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/BIO-
> SAXS_data/EPN_24196/reduced_data/standard_mode_reduction/1E4_12mgml_2565fa7c_E12k4_D750/DENSS/A_S_SM_1E4_12mgml_2565fa7c_E12k4_D750_average.mrc
> format mrc

Opened A_S_SM_1E4_12mgml_2565fa7c_E12k4_D750_average.mrc as #1, grid size
32,32,32, pixel 5.16, shown at level 0.0147, step 1, values float32  

> select clear

> volume #1 style mesh

> volume #1 style surface

> select clear

> graphics silhouettes width 1

> open /Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/BIO-
> SAXS_data/AvrStb6_dimer_refine_027.pdb

Chain information for AvrStb6_dimer_refine_027.pdb #2  
---  
Chain | Description  
A B | No description available  
  
Computing secondary structure  

> select clear

> select add #1

2 models selected  

> transparency #1.1 30

> select clear

> select add #2

1823 atoms, 1798 bonds, 189 residues, 1 model selected  

> ui mousemode right ""translate selected models""

> view matrix models #2,1,0,0,8.275,0,1,0,-23.095,0,0,1,-10.542

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,0.91544,0.27667,0.29228,-10.872,0.35654,-0.22063,-0.90785,39.061,-0.18669,0.93529,-0.30062,54.939

> view matrix models
> #2,0.65175,-0.71381,0.2563,21.516,0.42835,0.067567,-0.90108,29.831,0.62589,0.69707,0.3498,-14.075

> view matrix models
> #2,0.65203,-0.59289,0.47259,6.5335,0.46846,-0.17507,-0.86596,31.084,0.59616,0.78603,0.16359,-4.0796

> ui mousemode right ""translate selected models""

> view matrix models
> #2,0.65203,-0.59289,0.47259,-40.333,0.46846,-0.17507,-0.86596,19.815,0.59616,0.78603,0.16359,-42.216

> view matrix models
> #2,0.65203,-0.59289,0.47259,-40.253,0.46846,-0.17507,-0.86596,19.671,0.59616,0.78603,0.16359,-42.971

> view matrix models
> #2,0.65203,-0.59289,0.47259,-39.94,0.46846,-0.17507,-0.86596,32.422,0.59616,0.78603,0.16359,-43.949

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,0.25826,0.823,0.50593,-53.486,0.0097598,-0.5259,0.85049,-41.229,0.96603,-0.21471,-0.14385,-20.567

> volume #1 level 0.1022

> view matrix models
> #2,-0.045261,-0.84852,-0.52722,54.4,-0.32686,-0.48613,0.81045,-25.452,-0.94399,0.20901,-0.25534,58.534

> volume #1 style image

> volume #1 style mesh

> graphics silhouettes false

> view matrix models
> #2,0.53251,-0.7834,-0.32049,16.321,0.26483,-0.20542,0.94216,-64.006,-0.80393,-0.58658,0.098078,48.378

> volume #1 change image level -8.272e-05,0 level 0.01465,0.8 level 1.097,1

> volume #1 level 0.0347

> view matrix models
> #2,-0.74986,-0.57393,-0.32913,66.936,-0.061018,-0.43536,0.89819,-43.018,-0.65878,0.69359,0.29144,4.7179

> ui mousemode right ""translate selected models""

> view matrix models
> #2,-0.74986,-0.57393,-0.32913,56.842,-0.061018,-0.43536,0.89819,-42.718,-0.65878,0.69359,0.29144,-0.19789

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,-0.41694,-0.54058,-0.73071,65.785,-0.49801,-0.53665,0.68118,-9.252,-0.76036,0.64791,-0.045462,24.983

> ui mousemode right ""translate selected models""

> view matrix models
> #2,-0.41694,-0.54058,-0.73071,71.941,-0.49801,-0.53665,0.68118,-7.1044,-0.76036,0.64791,-0.045462,29.42

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,-0.49422,-0.39972,-0.77199,74.833,-0.53954,-0.55526,0.63292,-2.0958,-0.68164,0.72932,0.058754,18.237

> view matrix models
> #2,-0.43699,-0.46544,-0.76968,73.597,-0.47677,-0.60574,0.637,-3.9779,-0.76271,0.64532,0.042795,24.312

> ui mousemode right ""translate selected models""

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,-0.5266,-0.48532,-0.69796,73.517,-0.39084,-0.59089,0.70575,-12.011,-0.75494,0.64445,0.12148,19.312

> view matrix models
> #2,-0.55273,-0.42683,-0.71575,74.504,-0.43485,-0.58495,0.68464,-9.0102,-0.71091,0.68967,0.13771,15.57

> view matrix models
> #2,-0.80412,0.19628,-0.56113,63.574,-0.59443,-0.27608,0.75527,-12.705,-0.0066742,0.94088,0.33867,-31.169

> ui mousemode right ""translate selected models""

> view matrix models
> #2,-0.80412,0.19628,-0.56113,65.259,-0.59443,-0.27608,0.75527,-14.404,-0.0066742,0.94088,0.33867,-32.835

> volume #1 level 0.1083

> volume #1 level 0.02475

> view matrix models
> #2,-0.80412,0.19628,-0.56113,65.065,-0.59443,-0.27608,0.75527,-12.498,-0.0066742,0.94088,0.33867,-32.665

> view matrix models
> #2,-0.80412,0.19628,-0.56113,65.708,-0.59443,-0.27608,0.75527,-13.938,-0.0066742,0.94088,0.33867,-33.398

> volume #1 level 0.1202

> view matrix models
> #2,-0.80412,0.19628,-0.56113,65.2,-0.59443,-0.27608,0.75527,-14.163,-0.0066742,0.94088,0.33867,-32.963

> volume #1 level 0.02674

> view matrix models
> #2,-0.80412,0.19628,-0.56113,65.522,-0.59443,-0.27608,0.75527,-13.434,-0.0066742,0.94088,0.33867,-32.971

> volume #1 level 0.07249

> view matrix models
> #2,-0.80412,0.19628,-0.56113,64.605,-0.59443,-0.27608,0.75527,-14.717,-0.0066742,0.94088,0.33867,-32.792

> hide sel atoms

> select clear

> volume #1 level 0.1361

> select add #2

1823 atoms, 1798 bonds, 189 residues, 1 model selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,0.80586,0.35903,0.47084,-68.308,-0.47643,-0.078982,0.87566,-30.857,0.35157,-0.92998,0.1074,3.5351

> view matrix models
> #2,-0.36173,0.93143,0.039928,-4.7517,-0.71726,-0.30541,0.62631,-1.242,0.59555,0.19791,0.77855,-69.517

> view matrix models
> #2,-0.40095,0.91439,0.055934,-3.7021,-0.59714,-0.30717,0.74099,-13.125,0.69474,0.2637,0.66918,-68.523

> ui mousemode right ""translate selected models""

> view matrix models
> #2,-0.40095,0.91439,0.055934,-3.2019,-0.59714,-0.30717,0.74099,-13.575,0.69474,0.2637,0.66918,-70.244

> view matrix models
> #2,-0.40095,0.91439,0.055934,-4.1602,-0.59714,-0.30717,0.74099,-12.568,0.69474,0.2637,0.66918,-69.67

> view matrix models
> #2,-0.40095,0.91439,0.055934,-3.9173,-0.59714,-0.30717,0.74099,-12.615,0.69474,0.2637,0.66918,-69.748

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,-0.32818,0.93867,-0.10587,2.1551,-0.68898,-0.16118,0.70663,-9.6222,0.64623,0.30484,0.69962,-70.338

> select clear

> ui mousemode right ""translate selected models""

> select add #2

1823 atoms, 1798 bonds, 189 residues, 1 model selected  

> view matrix models
> #2,-0.32818,0.93867,-0.10587,2.2718,-0.68898,-0.16118,0.70663,-10.671,0.64623,0.30484,0.69962,-70.789

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,-0.34632,0.93305,-0.09739,2.6475,-0.63103,-0.15488,0.76014,-16.439,0.69417,0.32471,0.64242,-69.81

> ui mousemode right ""translate selected models""

> view matrix models
> #2,-0.34632,0.93305,-0.09739,2.3845,-0.63103,-0.15488,0.76014,-15.042,0.69417,0.32471,0.64242,-69.686

> volume #1 level 0.1421

> volume #1 step 2

> volume #1 step 16

> volume #1 step 1

> volume #1 level 0.1003

> view matrix models
> #2,-0.34632,0.93305,-0.09739,1.6883,-0.63103,-0.15488,0.76014,-16.975,0.69417,0.32471,0.64242,-69.296

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,-0.32921,0.93498,-0.13205,2.9911,-0.6778,-0.13662,0.72244,-13.117,0.65743,0.32734,0.6787,-69.956

> view matrix models
> #2,-0.3479,0.91047,-0.22364,9.7334,-0.6593,-0.067994,0.7488,-16.854,0.66655,0.40795,0.62392,-68.703

> ui mousemode right ""translate selected models""

> view matrix models
> #2,-0.3479,0.91047,-0.22364,9.5561,-0.6593,-0.067994,0.7488,-15.297,0.66655,0.40795,0.62392,-69.256

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,-0.33533,0.91917,-0.20661,7.8338,-0.6611,-0.073337,0.74671,-14.989,0.6712,0.38698,0.63225,-69.526

> view matrix models
> #2,-0.35254,0.9171,-0.18612,7.3828,-0.633,-0.08722,0.76922,-17.239,0.68922,0.38899,0.61128,-69.08

> ui mousemode right ""translate selected models""

> view matrix models
> #2,-0.35254,0.9171,-0.18612,7.6222,-0.633,-0.08722,0.76922,-18.172,0.68922,0.38899,0.61128,-69.335

> view matrix models
> #2,-0.35254,0.9171,-0.18612,7.2261,-0.633,-0.08722,0.76922,-16.95,0.68922,0.38899,0.61128,-69.075

> view matrix models
> #2,-0.35254,0.9171,-0.18612,7.243,-0.633,-0.08722,0.76922,-17.697,0.68922,0.38899,0.61128,-69.196

> view matrix models
> #2,-0.35254,0.9171,-0.18612,7.9445,-0.633,-0.08722,0.76922,-17.754,0.68922,0.38899,0.61128,-67.947

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,0.4043,0.79509,0.45208,-59.657,0.59904,0.14332,-0.78779,18.237,-0.69115,0.58931,-0.41835,47.792

> view matrix models
> #2,0.31151,0.75436,0.57784,-62.403,0.60044,0.31505,-0.73499,11.57,-0.7365,0.57592,-0.3548,46.194

> view matrix models
> #2,0.27978,0.73403,0.61881,-63.092,0.59662,0.37205,-0.71107,9.1576,-0.75218,0.56814,-0.33385,45.766

> view matrix models
> #2,0.10746,0.74992,0.65275,-58.141,0.74551,0.3736,-0.55194,-6.6572,-0.65778,0.54594,-0.51892,53.246

> view matrix models
> #2,0.1502,0.79191,0.59188,-57.17,0.77832,0.27444,-0.56471,-5.2869,-0.60963,0.54549,-0.57514,54.568

> view matrix models
> #2,0.61813,0.77599,0.12551,-48.862,-0.27407,0.063106,0.95964,-47.321,0.73675,-0.62758,0.25169,-28.041

> view matrix models
> #2,0.63368,0.76643,0.10507,-48.11,-0.30966,0.12684,0.94235,-46.069,0.70892,-0.62968,0.31771,-30.755

> view matrix models
> #2,0.62536,0.77137,0.11795,-48.625,-0.30637,0.10369,0.94625,-45.975,0.71768,-0.62788,0.30116,-30.176

> view matrix models
> #2,0.69795,0.6897,0.19284,-54.513,-0.33758,0.079379,0.93794,-43.669,0.63159,-0.71973,0.28823,-23.911

> ui mousemode right ""translate selected models""

> view matrix models
> #2,0.69795,0.6897,0.19284,-52.595,-0.33758,0.079379,0.93794,-43.879,0.63159,-0.71973,0.28823,-26.114

> view matrix models
> #2,0.69795,0.6897,0.19284,-54.492,-0.33758,0.079379,0.93794,-44.103,0.63159,-0.71973,0.28823,-27.327

> view matrix models
> #2,0.69795,0.6897,0.19284,-54.72,-0.33758,0.079379,0.93794,-44.655,0.63159,-0.71973,0.28823,-29.207

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,0.7283,0.68181,0.068635,-48.444,-0.34583,0.27924,0.89578,-45.822,0.59159,-0.67613,0.43917,-37.387

> view matrix models
> #2,0.90889,-0.41419,0.04853,-32.799,-0.27509,-0.50802,0.81624,-28.208,-0.31343,-0.75522,-0.57568,62.983

> view matrix models
> #2,0.78283,-0.59619,-0.17816,-10.287,-0.046101,-0.34111,0.93889,-48.573,-0.62053,-0.72678,-0.29451,58.653

> ui mousemode right ""translate selected models""

> view matrix models
> #2,0.78283,-0.59619,-0.17816,-11.12,-0.046101,-0.34111,0.93889,-47.976,-0.62053,-0.72678,-0.29451,59.985

> view matrix models
> #2,0.78283,-0.59619,-0.17816,-11.216,-0.046101,-0.34111,0.93889,-46.866,-0.62053,-0.72678,-0.29451,59.771

> view matrix models
> #2,0.78283,-0.59619,-0.17816,-11.265,-0.046101,-0.34111,0.93889,-47.579,-0.62053,-0.72678,-0.29451,60.072

> view matrix models
> #2,0.78283,-0.59619,-0.17816,-8.5839,-0.046101,-0.34111,0.93889,-47.073,-0.62053,-0.72678,-0.29451,63.483

> view matrix models
> #2,0.78283,-0.59619,-0.17816,-9.336,-0.046101,-0.34111,0.93889,-46.047,-0.62053,-0.72678,-0.29451,63.222

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,0.77851,-0.62046,-0.094627,-13.642,-0.083062,-0.25129,0.96434,-47.81,-0.62211,-0.74289,-0.24717,60.792

> ui mousemode right ""translate selected models""

> view matrix models
> #2,0.77851,-0.62046,-0.094627,-13.99,-0.083062,-0.25129,0.96434,-46.279,-0.62211,-0.74289,-0.24717,60.555

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,0.75154,-0.65945,-0.017724,-16.645,-0.24914,-0.3086,0.91798,-35.333,-0.61083,-0.68548,-0.39622,67.803

> view matrix models
> #2,0.71362,-0.69047,0.11835,-22.524,-0.3037,-0.15268,0.94046,-37.506,-0.63128,-0.70707,-0.31865,64.481

> ui mousemode right ""translate selected models""

> view matrix models
> #2,0.71362,-0.69047,0.11835,-21.642,-0.3037,-0.15268,0.94046,-39.631,-0.63128,-0.70707,-0.31865,62.563

> volume #1 level 0.1739

> volume #1 level 0.02475

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,0.74211,0.55337,0.37823,-63.404,-0.58008,0.2475,0.77605,-26.203,0.33583,-0.79532,0.50467,-25.65

> ui mousemode right ""translate selected models""

> view matrix models
> #2,0.74211,0.55337,0.37823,-66.792,-0.58008,0.2475,0.77605,-22.082,0.33583,-0.79532,0.50467,-25.549

> view matrix models
> #2,0.74211,0.55337,0.37823,-63.831,-0.58008,0.2475,0.77605,-26.038,0.33583,-0.79532,0.50467,-25.745

> select clear

Alignment identifier is 1  

> select /A-B:7

30 atoms, 28 bonds, 2 residues, 1 model selected  

> select /A-B:7-10

86 atoms, 84 bonds, 8 residues, 1 model selected  

> select /A-B:7

30 atoms, 28 bonds, 2 residues, 1 model selected  

> select /A-B:7-8

52 atoms, 50 bonds, 4 residues, 1 model selected  

> select /A-B:7

30 atoms, 28 bonds, 2 residues, 1 model selected  

> select /A-B:7-9

72 atoms, 70 bonds, 6 residues, 1 model selected  

> select /A-B:7

30 atoms, 28 bonds, 2 residues, 1 model selected  

> select /A-B:7-8

52 atoms, 50 bonds, 4 residues, 1 model selected  

> hide sel cartoons

> select /A-B:71

28 atoms, 28 bonds, 2 residues, 1 model selected  

> select /A-B:69-71

62 atoms, 62 bonds, 6 residues, 1 model selected  

> select /A-B:70

20 atoms, 18 bonds, 2 residues, 1 model selected  

> select /A-B:70-71

48 atoms, 48 bonds, 4 residues, 1 model selected  

> hide sel cartoons

> select clear

> select add #2

1823 atoms, 1798 bonds, 189 residues, 1 model selected  

> view matrix models
> #2,0.74211,0.55337,0.37823,-65.446,-0.58008,0.2475,0.77605,-28.801,0.33583,-0.79532,0.50467,-23.527

> view matrix models
> #2,0.74211,0.55337,0.37823,-65.26,-0.58008,0.2475,0.77605,-28.585,0.33583,-0.79532,0.50467,-23.825

> view matrix models
> #2,0.74211,0.55337,0.37823,-62.861,-0.58008,0.2475,0.77605,-28.611,0.33583,-0.79532,0.50467,-23.36

> view matrix models
> #2,0.74211,0.55337,0.37823,-64.378,-0.58008,0.2475,0.77605,-28.606,0.33583,-0.79532,0.50467,-21.847

> view matrix models
> #2,0.74211,0.55337,0.37823,-65.692,-0.58008,0.2475,0.77605,-28.195,0.33583,-0.79532,0.50467,-22.858

> view matrix models
> #2,0.74211,0.55337,0.37823,-65.548,-0.58008,0.2475,0.77605,-29.362,0.33583,-0.79532,0.50467,-23.863

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,0.87419,0.43634,0.21308,-58.816,-0.35897,0.28519,0.88871,-46.035,0.32701,-0.85339,0.40594,-16.431

> view matrix models
> #2,0.84001,0.13513,0.52547,-69.877,-0.54255,0.20147,0.8155,-32.336,0.0043287,-0.97013,0.24255,9.0988

> view matrix models
> #2,0.49276,0.83329,0.25063,-53.276,-0.61867,0.13295,0.77432,-25.322,0.61191,-0.53661,0.58105,-45.16

> view matrix models
> #2,0.81289,0.53929,0.21996,-58.773,-0.4223,0.28567,0.86026,-41.717,0.4011,-0.79218,0.45996,-23.976

> view matrix models
> #2,-0.70647,0.70775,0.00096513,14.019,0.53598,0.5359,-0.65233,3.479,-0.4622,-0.46033,-0.75793,77.735

> view matrix models
> #2,-0.96137,-0.13888,-0.23767,56.074,0.16022,0.41977,-0.89338,35.83,0.22384,-0.89694,-0.3813,35.657

> view matrix models
> #2,-0.79388,-0.45934,-0.39844,65.215,0.14966,0.48749,-0.86021,32.914,0.58936,-0.74254,-0.31826,13.559

> view matrix models
> #2,0.64559,-0.74911,-0.14852,-3.6279,0.46978,0.54288,-0.69613,8.6992,0.6021,0.37964,0.70239,-70.638

> volume #1 level 0.1341

> view matrix models
> #2,-0.75337,-0.62483,-0.20498,55.372,0.14015,0.15198,-0.9784,47.183,0.64249,-0.76582,-0.026923,-5.5365

> view matrix models
> #2,-0.22882,-0.97245,0.044522,25.772,-0.20425,0.0032445,-0.97891,64.562,0.9518,-0.23309,-0.19937,-18.967

> view matrix models
> #2,-0.15812,-0.98603,0.052388,22.64,-0.19868,-0.020201,-0.97986,64.864,0.96723,-0.16534,-0.19271,-21.385

> view matrix models
> #2,-0.94786,-0.17688,-0.26508,57.92,0.05406,0.73052,-0.68075,21.247,0.31406,-0.65959,-0.68287,45.043

> view matrix models
> #2,-0.16798,-0.98031,-0.10379,32.24,0.1886,0.071381,-0.97946,46.873,0.96758,-0.1841,0.17289,-42.804

> view matrix models
> #2,-0.16614,-0.98602,-0.012549,26.843,0.33529,-0.044517,-0.94106,40.846,0.92735,-0.16056,0.338,-51.449

> volume #1 level 0.006849

> volume #1 level 0.09437

> ui mousemode right ""translate selected models""

> view matrix models
> #2,-0.16614,-0.98602,-0.012549,27.014,0.33529,-0.044517,-0.94106,43.332,0.92735,-0.16056,0.338,-52.255

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,-0.21049,-0.87015,-0.44558,52.303,-0.006166,0.45696,-0.88947,44.244,0.97758,-0.18448,-0.10155,-27.664

> view matrix models
> #2,-0.34314,-0.80454,-0.48473,58.816,0.027719,0.50717,-0.8614,40.141,0.93887,-0.30902,-0.15173,-20.529

> view matrix models
> #2,-0.060577,-0.91133,-0.4072,44.621,-0.0201,0.40898,-0.91232,47.162,0.99796,-0.047081,-0.043093,-34.792

> view matrix models
> #2,-0.19828,-0.97283,-0.11956,34.458,0.19017,0.081479,-0.97836,49.023,0.96152,-0.21672,0.16885,-42.452

> view matrix models
> #2,-0.29686,-0.93294,-0.2037,42.759,0.29276,0.11412,-0.94935,42.364,0.90894,-0.34146,0.23925,-41.921

> view matrix models
> #2,-0.3796,-0.90335,-0.19966,45.356,0.23343,0.11531,-0.96551,45.77,0.89522,-0.41311,0.16709,-35.593

> view matrix models
> #2,-0.39343,-0.9053,-0.16011,43.614,0.23883,0.067528,-0.96871,46.709,0.88779,-0.41936,0.18965,-36.5

> view matrix models
> #2,-0.37338,-0.89635,-0.23906,47.303,0.24768,0.15202,-0.95684,43.913,0.894,-0.41647,0.16524,-35.363

> view matrix models
> #2,-0.54365,-0.81352,-0.20646,50.754,0.14249,0.15296,-0.97791,49.523,0.82713,-0.56106,0.032763,-21.745

> ui mousemode right ""translate selected models""

> view matrix models
> #2,-0.54365,-0.81352,-0.20646,51.267,0.14249,0.15296,-0.97791,50.14,0.82713,-0.56106,0.032763,-21.03

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,-0.95306,-0.23881,-0.18612,55.377,0.066915,0.4334,-0.89871,42.854,0.29528,-0.86899,-0.39708,32.966

> view matrix models
> #2,-0.95139,0.064309,-0.30119,55.993,0.3073,0.26314,-0.91451,37.267,0.020443,-0.96261,-0.27011,38.734

> view matrix models
> #2,-0.9238,0.27869,-0.26252,48.177,0.34,0.28194,-0.89717,34.491,-0.17602,-0.91806,-0.35522,51.067

> view matrix models
> #2,-0.95121,0.25091,-0.17957,44.939,0.26484,0.36532,-0.89241,35.635,-0.15831,-0.89643,-0.41395,53.39

> volume #1 level 0.0347

> volume #1 level 0.1003

> ui mousemode right ""translate selected models""

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,-0.93909,0.24057,-0.24544,48.57,0.32404,0.38183,-0.86557,31.238,-0.11451,-0.89237,-0.43653,52.832

> volume #1 level 0.1162

> select clear

> open /Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/BIO-
> SAXS_data/EPN_24196/reduced_data/standard_mode_reduction/1E4_12mgml_2565fa7c_E12k4_D750/DENSS_20_slow/A_S_SM_1E4_12mgml_2565fa7c_E12k4_D750_refine_aligned.mrc

Opened A_S_SM_1E4_12mgml_2565fa7c_E12k4_D750_refine_aligned.mrc as #3, grid
size 64,64,64, pixel 2.58, shown at level 0.00127, step 1, values float32  

> volume #3 level 0.05394

> select add #3

2 models selected  

> view matrix models
> #3,0.90439,-0.32834,0.27253,0.55824,0.30016,0.03557,-0.95322,1.122,0.30329,0.94389,0.13073,-1.6301

> view matrix models
> #3,0.90114,-0.28883,0.3233,0.53428,0.34884,0.0403,-0.93632,1.1979,0.25741,0.95653,0.13707,-1.7097

> view matrix models
> #3,0.90998,-0.25742,0.32508,0.50189,0.36592,0.12972,-0.92156,1.1016,0.19506,0.95755,0.21223,-1.7428

> volume #3 level 0.01005

> view matrix models
> #3,0.85452,-0.29737,0.42588,0.71244,0.4528,0.024725,-0.89127,1.7863,0.2545,0.95444,0.15578,-1.6904

> view matrix models
> #3,0.82766,-0.42728,0.36389,0.72372,0.4185,0.037858,-0.90743,1.571,0.37395,0.90333,0.21015,-0.93365

> view matrix models
> #3,0.82868,-0.44662,0.33737,0.68869,0.4024,0.056409,-0.91373,1.444,0.38905,0.89295,0.22646,-0.79796

> ui mousemode right ""translate selected models""

> view matrix models
> #3,0.82868,-0.44662,0.33737,2.7517,0.4024,0.056409,-0.91373,0.90906,0.38905,0.89295,0.22646,2.1876

> volume #3 level 0.02761

> volume #3 style mesh

> select clear

> hide #!1 models

> color #3 black models

> color #3 #942193ff models

> color #3 #0433ffff models

> color #3 #9437ffff models

> color #3 #ff2600ff models

> color #3 #d6d6d6ff models

> color #3 #919191ff models

> color #3 #797979ff models

> color #3 silver models

> color #3 darkgrey models

> show #!1 models

> hide #!3 models

> show #!3 models

> volume #3 level -0.007502

> hide #!3 models

> ui mousemode right ""rotate selected models""

> select add #2

1823 atoms, 1798 bonds, 189 residues, 1 model selected  

> view matrix models
> #2,-0.93051,0.25996,-0.25802,48.569,0.35574,0.47383,-0.80556,24.471,-0.087155,-0.84137,-0.53338,56.427

> view matrix models
> #2,-0.65984,0.74305,-0.1117,18.76,0.46661,0.28868,-0.83602,25.446,-0.58896,-0.60377,-0.5372,72.682

> view matrix models
> #2,-0.65535,0.74253,-0.13843,20.177,0.50482,0.29426,-0.81152,22.284,-0.56185,-0.60171,-0.56769,73.329

> view matrix models
> #2,-0.81072,0.54348,-0.21764,35.41,0.43735,0.31511,-0.84228,26.497,-0.38917,-0.77803,-0.49316,65.298

> hide #2 models

> show #2 models

> select subtract #2

Nothing selected  

> select clear

> volume #1 level 0.09437

> ui mousemode right ""translate selected models""

> hide #2 models

> show #2 models

> select add #2

1823 atoms, 1798 bonds, 189 residues, 1 model selected  

> view matrix models
> #2,-0.81072,0.54348,-0.21764,35.713,0.43735,0.31511,-0.84228,24.938,-0.38917,-0.77803,-0.49316,64.981

> hide #2 models

> show #2 models

> select subtract #2

Nothing selected  

> color #2 #919191ff

> color #2 #008f00ff

> color #2 #919191ff

> color #2 #797979ff

> color #2 #919191ff

> color #2 darkgrey

> color #2 silver

> color #2 #919191ff

> color #2 #929292ff

> color #1 #797979ff models

> color #1 #919191ff models

> color #1 #797979ff models

> color #1 #5e5e5eff models

> color #1 #797979ff models

> color #1 #919191ff models

> select clear

> volume #1 level 0.1123

> volume #1 level 0.1819

> volume #1 level 0.1262

> volume #1 level 0.08243

> select add #2

1823 atoms, 1798 bonds, 189 residues, 1 model selected  

> view matrix models
> #2,-0.81072,0.54348,-0.21764,35.569,0.43735,0.31511,-0.84228,25.584,-0.38917,-0.77803,-0.49316,65.236

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,-0.076082,0.97165,0.22384,-30.001,0.62727,0.22114,-0.74674,13.908,-0.77507,0.083593,-0.62632,71.673

> select subtract #2

Nothing selected  

> select clear

> volume #1 level 0.168

> select clear

> select add #2

1823 atoms, 1798 bonds, 189 residues, 1 model selected  

> view matrix models
> #2,-0.084348,0.96935,0.23075,-30.022,0.64497,0.22963,-0.72889,11.936,-0.75954,0.087344,-0.64457,72.039

> view matrix models
> #2,-0.095717,0.89863,0.42813,-39.871,0.61133,0.3925,-0.68718,7.5333,-0.78557,0.19595,-0.58693,67.475

> view matrix models
> #2,-0.16416,0.91475,0.36916,-33.84,0.60904,0.38838,-0.69154,7.9715,-0.77596,0.11132,-0.62088,70.822

> view matrix models
> #2,-0.17183,0.91089,0.37518,-33.801,0.62501,0.39518,-0.67319,6.0759,-0.76147,0.11882,-0.63722,71.04

> view matrix models
> #2,-0.53276,0.84625,0.0055281,4.5488,-0.58212,-0.3712,0.72342,-11.353,0.61425,0.38219,0.69038,-70.633

> view matrix models
> #2,-0.47611,0.8724,-0.11061,8.5821,-0.5465,-0.19499,0.81444,-21.845,0.68895,0.44822,0.56961,-67.886

> view matrix models
> #2,-0.47923,0.87645,-0.046643,4.8173,-0.5294,-0.24626,0.81185,-21.358,0.70006,0.41376,0.582,-68.385

> view matrix models
> #2,-0.45136,0.88961,-0.069751,4.7676,-0.54197,-0.2112,0.81343,-21.643,0.7089,0.40495,0.57747,-68.303

> view matrix models
> #2,-0.42339,0.90019,-0.10199,5.3101,-0.68646,-0.24532,0.68454,-7.2606,0.59119,0.35984,0.72181,-71.091

> view matrix models
> #2,-0.42612,0.89919,-0.099372,5.2879,-0.67465,-0.24267,0.69711,-8.5548,0.60272,0.36409,0.71005,-70.956

> ui mousemode right ""translate selected models""

> view matrix models
> #2,-0.42612,0.89919,-0.099372,5.4026,-0.67465,-0.24267,0.69711,-9.7406,0.60272,0.36409,0.71005,-71.422

> select subtract #2

Nothing selected  

> select clear

> ui mousemode right ""rotate selected models""

> select add #2

1823 atoms, 1798 bonds, 189 residues, 1 model selected  

> view matrix models
> #2,-0.43109,0.89722,-0.095713,5.4316,-0.65373,-0.23745,0.71851,-11.992,0.62193,0.37231,0.6889,-71.128

> select subtract #2

Nothing selected  

> ui mousemode right ""translate selected models""

> select add #2

1823 atoms, 1798 bonds, 189 residues, 1 model selected  

> view matrix models
> #2,-0.43109,0.89722,-0.095713,5.3511,-0.65373,-0.23745,0.71851,-12.464,0.62193,0.37231,0.6889,-70.662

> hide #!3 models

> volume #1 level 0.1859

> select clear

> volume #1 level 0.286

> volume #1 level 0.186

> color #1 #008f00ff models

> color #1 #fffb00ff models

> color #1 darkgrey models

> color #2 #fffb00ff

> color #2 #fffc79ff

> color #2 #ffd479ff

> color #2 #fffc79ff

> color #2 #d4fb79ff

> color #2 #ebebebff

> color #2 #d6d6d6ff

> color #2 silver

> color #2 darkgrey

> color #2 #929292ff

> color #2 darkgrey

> color #1 black models

> color #1 #424242ff models

> color #1 #797979ff models

> color #1 #929292ff models

> select clear

> volume #1 level 0.176

> volume #1 level 0.196

> volume #1 level 0.199

> select add #2

1823 atoms, 1798 bonds, 189 residues, 1 model selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,-0.44073,0.89306,-0.090513,5.5266,-0.62073,-0.23038,0.74941,-15.821,0.64842,0.38647,0.65589,-70.085

> ui mousemode right ""translate selected models""

> view matrix models
> #2,-0.44073,0.89306,-0.090513,5.3586,-0.62073,-0.23038,0.74941,-14.772,0.64842,0.38647,0.65589,-69.805

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,-0.43095,0.89704,-0.097985,5.3165,-0.6493,-0.23285,0.72401,-12.02,0.62665,0.37564,0.6828,-70.283

> ui mousemode right ""translate selected models""

> view matrix models
> #2,-0.43095,0.89704,-0.097985,5.6796,-0.6493,-0.23285,0.72401,-12.965,0.62665,0.37564,0.6828,-71.117

> view matrix models
> #2,-0.43095,0.89704,-0.097985,5.4149,-0.6493,-0.23285,0.72401,-12.877,0.62665,0.37564,0.6828,-70.315

> view matrix models
> #2,-0.43095,0.89704,-0.097985,5.4984,-0.6493,-0.23285,0.72401,-12.89,0.62665,0.37564,0.6828,-70.577

> view matrix models
> #2,-0.43095,0.89704,-0.097985,5.4888,-0.6493,-0.23285,0.72401,-12.815,0.62665,0.37564,0.6828,-70.588

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,-0.42984,0.89753,-0.098356,5.4545,-0.65201,-0.23319,0.72146,-12.543,0.6246,0.37424,0.68544,-70.632

> view matrix models
> #2,0.72897,0.67465,0.11595,-50.959,-0.28779,0.14835,0.94613,-48.843,0.62111,-0.72307,0.3023,-25.316

> view matrix models
> #2,-0.36726,0.88871,-0.27443,13.524,-0.68642,-0.059863,0.72474,-14.837,0.62766,0.45454,0.63201,-69.211

> ui mousemode right ""translate selected models""

> view matrix models
> #2,-0.36726,0.88871,-0.27443,13.257,-0.68642,-0.059863,0.72474,-14.235,0.62766,0.45454,0.63201,-68.693

> select clear

> ui mousemode right ""rotate selected models""

> select add #2

1823 atoms, 1798 bonds, 189 residues, 1 model selected  

> view matrix models
> #2,-0.35924,0.89032,-0.27979,13.21,-0.7067,-0.063715,0.70464,-12.115,0.60952,0.45086,0.65208,-69.06

> ui mousemode right ""translate selected models""

> view matrix models
> #2,-0.35924,0.89032,-0.27979,13.406,-0.7067,-0.063715,0.70464,-11.986,0.60952,0.45086,0.65208,-69.65

> select subtract #2

Nothing selected  

> ui mousemode right ""rotate selected models""

> select add #2

1823 atoms, 1798 bonds, 189 residues, 1 model selected  

> view matrix models
> #2,-0.38281,0.70266,-0.59978,37.274,-0.84038,-0.5345,-0.089808,50.497,-0.38369,0.46966,0.79511,-37.26

> view matrix models
> #2,-0.26922,0.56303,-0.78135,46.214,-0.82765,0.27958,0.48664,-0.95674,0.49245,0.77771,0.39073,-55.863

> view matrix models
> #2,-0.41461,-0.73281,-0.53952,64.232,-0.65936,-0.16669,0.73311,-13.555,-0.62717,0.65969,-0.41408,41.049

> view matrix models
> #2,0.57268,-0.81626,0.07588,-11.79,-0.3511,-0.16058,0.92246,-37.78,-0.74079,-0.55492,-0.37855,68.386

> view matrix models
> #2,0.5712,-0.81739,0.0749,-11.647,-0.35131,-0.16099,0.92231,-37.754,-0.74183,-0.55314,-0.37911,68.426

> view matrix models
> #2,0.26197,-0.9629,-0.064823,12.498,-0.1515,-0.10737,0.98261,-50.746,-0.95311,-0.2476,-0.17401,58.768

> view matrix models
> #2,0.28078,-0.95711,-0.071408,11.991,-0.22437,-0.1378,0.96471,-46.03,-0.93318,-0.25485,-0.25344,62.82

> view matrix models
> #2,0.28266,-0.95661,-0.070694,11.86,-0.22403,-0.1375,0.96483,-46.058,-0.93269,-0.25688,-0.25317,62.826

> select clear

> select add #2

1823 atoms, 1798 bonds, 189 residues, 1 model selected  

> view matrix models
> #2,0.27601,-0.95878,-0.067489,11.99,-0.18811,-0.12274,0.97445,-48.425,-0.94257,-0.25626,-0.21423,60.903

> select clear

> select add #2

1823 atoms, 1798 bonds, 189 residues, 1 model selected  

> ui mousemode right ""translate selected models""

> view matrix models
> #2,0.27601,-0.95878,-0.067489,12.105,-0.18811,-0.12274,0.97445,-49.331,-0.94257,-0.25626,-0.21423,60.712

> select subtract #2

Nothing selected  

> volume #1 level 0.1354

> select add #2

1823 atoms, 1798 bonds, 189 residues, 1 model selected  

> view matrix models
> #2,0.27601,-0.95878,-0.067489,11.743,-0.18811,-0.12274,0.97445,-45.93,-0.94257,-0.25626,-0.21423,61.16

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,0.26169,-0.96512,-0.0071889,8.8737,-0.27926,-0.082848,0.95663,-41.891,-0.92387,-0.24834,-0.2912,64.807

> view matrix models
> #2,-0.035977,-0.9571,-0.28751,37.791,-0.050686,-0.28557,0.95702,-47.29,-0.99807,0.049004,-0.038238,46.765

> view matrix models
> #2,0.35137,-0.93581,0.028388,2.4282,-0.25569,-0.066748,0.96445,-43.665,-0.90064,-0.34614,-0.26273,64.136

> view matrix models
> #2,0.39555,-0.91755,-0.040398,4.3186,-0.20352,-0.13046,0.97034,-44.888,-0.89561,-0.3756,-0.23834,63.074

> ui mousemode right ""translate selected models""

> view matrix models
> #2,0.39555,-0.91755,-0.040398,5.0464,-0.20352,-0.13046,0.97034,-47.195,-0.89561,-0.3756,-0.23834,63.401

> view matrix models
> #2,0.39555,-0.91755,-0.040398,4.9786,-0.20352,-0.13046,0.97034,-47.153,-0.89561,-0.3756,-0.23834,63.196

> select clear

> volume #1 level 0.145

> volume #1 level 0.155

> graphics silhouettes true

> graphics silhouettes width 0.5

> graphics silhouettes width 0.6

> graphics silhouettes width 0.7

> graphics silhouettes width 0.8

> select clear

> lighting flat

> lighting soft

> lighting simple

> lighting full

> lighting flat

> lighting shadows true intensity 0.5

> lighting soft

> lighting shadows true intensity 0.5

> lighting soft

> ui mousemode right ""rotate selected models""

> select add #2

1823 atoms, 1798 bonds, 189 residues, 1 model selected  

> view matrix models
> #2,0.40195,-0.91481,-0.039464,4.601,-0.25621,-0.15374,0.95432,-43.534,-0.87909,-0.37348,-0.29618,65.912

> ui mousemode right ""translate selected models""

> view matrix models
> #2,0.40195,-0.91481,-0.039464,4.4932,-0.25621,-0.15374,0.95432,-42.647,-0.87909,-0.37348,-0.29618,65.627

> view matrix models
> #2,0.40195,-0.91481,-0.039464,4.451,-0.25621,-0.15374,0.95432,-42.319,-0.87909,-0.37348,-0.29618,65.366

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,0.57486,-0.81089,0.10955,-13.734,-0.28538,-0.073207,0.95562,-42.824,-0.76688,-0.58061,-0.27349,63.566

> ui mousemode right ""translate selected models""

> view matrix models
> #2,0.57486,-0.81089,0.10955,-13.705,-0.28538,-0.073207,0.95562,-42.949,-0.76688,-0.58061,-0.27349,64.475

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,0.57073,-0.81388,0.10894,-13.436,-0.25194,-0.047294,0.96659,-45.521,-0.78153,-0.57911,-0.23204,62.584

> view matrix models
> #2,0.57664,-0.80321,0.14948,-16.314,-0.27198,-0.016199,0.96217,-45.057,-0.7704,-0.59548,-0.2278,62.202

> view matrix models
> #2,0.58355,-0.80984,0.060278,-11.151,-0.22137,-0.087221,0.97128,-46.259,-0.78132,-0.58013,-0.23017,62.485

> view matrix models
> #2,0.58355,-0.80986,0.06001,-11.135,-0.22078,-0.087106,0.97143,-46.294,-0.78149,-0.58012,-0.22963,62.46

> view matrix models
> #2,0.47365,-0.87566,0.094267,-7.2668,-0.26187,-0.03783,0.96436,-45.168,-0.84088,-0.48145,-0.24723,63.968

> ui mousemode right ""translate selected models""

> view matrix models
> #2,0.47365,-0.87566,0.094267,-7.0143,-0.26187,-0.03783,0.96436,-45.913,-0.84088,-0.48145,-0.24723,63.068

> select clear

> volume #1 level 0.165

> volume #1 level 0.175

> volume #1 level 0.185

> volume #1 level 0.195

> color #2 #f6f6f6ff

> color #2 #942193ff

> color #2 #941751ff

> select /A

888 atoms, 902 bonds, 68 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel slate gray

> select /B

880 atoms, 896 bonds, 66 residues, 1 model selected  

> color sel light gray target c

> color sel silver target c

> select clear

> select /B

880 atoms, 896 bonds, 66 residues, 1 model selected  

> color sel gray target c

> color sel light gray target c

> color sel silver target c

> color sel gainsboro target c

> color sel silver target c

> select clear

> color #1 black models

> color #1 #212121ff models

> color #1 #424242ff models

> color #1 #5e5e5eff models

> color #1 #797979ff models

> select add #2

1823 atoms, 1798 bonds, 189 residues, 1 model selected  

> view matrix models
> #2,0.47365,-0.87566,0.094267,-6.1759,-0.26187,-0.03783,0.96436,-45.88,-0.84088,-0.48145,-0.24723,62.917

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,0.50678,-0.86127,0.037171,-4.4442,-0.18467,-0.066345,0.98056,-49.475,-0.84206,-0.5038,-0.19268,60.17

> select clear

> select /B

880 atoms, 896 bonds, 66 residues, 1 model selected  

> color sel black target c

> color sel light slate gray target c

> color sel slate gray target c

> color sel gray target c

> color sel gainsboro target c

> color sel light gray target c

> select clear

> lighting soft

> lighting flat

> select /B

880 atoms, 896 bonds, 66 residues, 1 model selected  

> color sel gray target c

> color sel silver target c

> color sel light gray target c

> color sel silver target c

> select clear

> select /B

880 atoms, 896 bonds, 66 residues, 1 model selected  

> color sel dark gray target c

> select clear

> volume #1 level 0.205

> save /Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/BIO-SAXS_data/1E4_DENSS_model.cxs

> save /Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/PhD/Manuscripts/01_Stb6-AvrStb6/Data/1E4-SAXS-
> model.png width 867 height 739 supersample 4 transparentBackground true

> hide #!1 models

> select clear

> show atoms

> ui tool show Contacts

> contacts saveFile /Users/u6290062/Downloads/1E4-contacts ignoreHiddenModels
> true select true reveal true

1110 contacts  

> close #1

> close #3

> close #2.1

> select clear

> ui tool show Contacts

> select /A

888 atoms, 902 bonds, 68 residues, 1 model selected  

> select add #2

1823 atoms, 1798 bonds, 189 residues, 1 model selected  

> contacts sel restrict both intraModel false intraMol false
> ignoreHiddenModels true select true reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: False
    
    0 contacts
    atom1  atom2  overlap  distance
    

  
No contacts  

> select clear

> hide atoms

> select /A-B:40

34 atoms, 34 bonds, 2 residues, 1 model selected  

> select /A-B:40

34 atoms, 34 bonds, 2 residues, 1 model selected  

> select /A-B:41

28 atoms, 26 bonds, 2 residues, 1 model selected  

> select /A-B:41

28 atoms, 26 bonds, 2 residues, 1 model selected  

> select /A-B:40

34 atoms, 34 bonds, 2 residues, 1 model selected  

> select /A-B:40-41

62 atoms, 62 bonds, 4 residues, 1 model selected  

> select /A-B:40-41

62 atoms, 62 bonds, 4 residues, 1 model selected  

> select /A-B:40-41

62 atoms, 62 bonds, 4 residues, 1 model selected  

> select clear

> select /A-B:40-41

62 atoms, 62 bonds, 4 residues, 1 model selected  

> select /A-B:40-41

62 atoms, 62 bonds, 4 residues, 1 model selected  

> show sel atoms

> select clear

> select /A-B:46-47

74 atoms, 74 bonds, 4 residues, 1 model selected  

> select /A-B:46-50

168 atoms, 172 bonds, 10 residues, 1 model selected  

> show sel atoms

> select clear

> select /A-B:60-61

66 atoms, 64 bonds, 4 residues, 1 model selected  

> select /A-B:60-62

104 atoms, 102 bonds, 6 residues, 1 model selected  

> show sel atoms

> select clear

> select /A

888 atoms, 902 bonds, 68 residues, 1 model selected  

> select /B

880 atoms, 896 bonds, 66 residues, 1 model selected  

> color sel silver target c

> color sel light gray target c

> color sel silver target ac

> color sel dim gray target ac

> color sel gray target ac

> color sel dark gray target ac

> select clear

> color byhetero

> select clear

> graphics silhouettes false

> graphics silhouettes true

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> lighting soft

> lighting shadows true intensity 0.5

> lighting soft

> graphics silhouettes width 1

> select clear

> select ::name=""HOH""

55 atoms, 55 residues, 1 model selected  

> show sel atoms

> select clear

> select /A-B:60

34 atoms, 32 bonds, 2 residues, 1 model selected  

> select /A-B:60-62

104 atoms, 102 bonds, 6 residues, 1 model selected  

> select /A-B:61-62

70 atoms, 68 bonds, 4 residues, 1 model selected  

> select /A-B:61-62

70 atoms, 68 bonds, 4 residues, 1 model selected  

> select clear

> show surfaces

> select clear

> hide surfaces

> select clear

> hide atoms

> select clear

> select /A-B:61-62

70 atoms, 68 bonds, 4 residues, 1 model selected  

> select /A-B:61-62

70 atoms, 68 bonds, 4 residues, 1 model selected  

> select /A-B:50

40 atoms, 40 bonds, 2 residues, 1 model selected  

> select /A-B:50

40 atoms, 40 bonds, 2 residues, 1 model selected  

> select /A-B:50,61-62

110 atoms, 108 bonds, 6 residues, 1 model selected  

> show sel atoms

> select clear

> show cartoons

> select clear

> hide atoms

> select add /B:21

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

> setattr #2:19-21 res ss_type )

Assigning ss_type attribute to 8 items  
Cannot set attribute 'ss_type' to ')'  

> setattr #2:19-21 res ss_type 0

Assigning ss_type attribute to 8 items  

> select clear

> show surfaces

> select clear

> transparency 50

> select clear

> transparency 70

> select clear

> save
> /Users/u6290062/Documents/PhD/Manuscripts/01_Stb6-AvrStb6/Data/1E4-dimer-
> crescent.png width 791 height 739 supersample 4 transparentBackground true

> select clear

> transparency 0

> select clear

> transparency 70

> select clear

> save
> /Users/u6290062/Documents/PhD/Manuscripts/01_Stb6-AvrStb6/Data/1E4-dimer-
> core.png width 791 height 739 supersample 4 transparentBackground true

> select clear

> transparency 0

> transparency 50

> select /A-B:61-62

70 atoms, 68 bonds, 4 residues, 1 model selected  

> select /A-B:61-62

70 atoms, 68 bonds, 4 residues, 1 model selected  

> select clear

> transparency 70

> select clear

> save
> /Users/u6290062/Documents/PhD/Manuscripts/01_Stb6-AvrStb6/Data/1E4-dimer-
> hydrophobic.png width 791 height 739 supersample 4 transparentBackground
> true

> select clear

> select /A-B:41

28 atoms, 26 bonds, 2 residues, 1 model selected  

> select /A-B:41

28 atoms, 26 bonds, 2 residues, 1 model selected  

> select /A-B:35,41

62 atoms, 58 bonds, 4 residues, 1 model selected  

> select /A-B:35,41

62 atoms, 58 bonds, 4 residues, 1 model selected  

> select clear

> select /A-B:41

28 atoms, 26 bonds, 2 residues, 1 model selected  

> select /A-B:41

28 atoms, 26 bonds, 2 residues, 1 model selected  

> show sel atoms

> select clear

> select /A-B:47

34 atoms, 32 bonds, 2 residues, 1 model selected  

> select /A-B:47

34 atoms, 32 bonds, 2 residues, 1 model selected  

> show sel atoms

> select clear

> ui tool show Distances

> select /B:41@CG2

1 atom, 1 residue, 1 model selected  

> select clear

> hide surfaces

> select /B:41@OG1

1 atom, 1 residue, 1 model selected  

> select add /B:47@NE2

2 atoms, 2 residues, 2 models selected  

> distance /B:41@OG1 /B:47@NE2

Distance between /B THR 41 OG1 and GLN 47 NE2: 4.764Å  

> select clear

> hide #1.1 models

> select clear

> select /B:47@OE1

1 atom, 1 residue, 1 model selected  

> select add /B:41@HG1

2 atoms, 2 residues, 2 models selected  

> distance /B:47@OE1 /B:41@HG1

Distance between /B GLN 47 OE1 and THR 41 HG1: 5.427Å  

> select clear

> select /A:41@OG1

1 atom, 1 residue, 1 model selected  
Drag select of 1 atoms  

> select /A:41@OG1

1 atom, 1 residue, 1 model selected  

> select add /A:47@NE2

2 atoms, 2 residues, 2 models selected  

> distance /A:41@OG1 /A:47@NE2

Distance between /A THR 41 OG1 and GLN 47 NE2: 4.772Å  

> select clear

> hide #!1 models

> select /A-B:47

34 atoms, 32 bonds, 2 residues, 1 model selected  

> select /A-B:47

34 atoms, 32 bonds, 2 residues, 1 model selected  

> select /A-B:28-33,36-41,56-60,64-68

606 atoms, 608 bonds, 44 residues, 1 model selected  

> select /A-B:41

28 atoms, 26 bonds, 2 residues, 1 model selected  

> select /A-B:41

28 atoms, 26 bonds, 2 residues, 1 model selected  

> hbonds sel reveal true

9 hydrogen bonds found  

> select add /A:48

48 atoms, 46 bonds, 3 residues, 3 models selected  

> show sel atoms

> select clear

> select /A-B:47

34 atoms, 32 bonds, 2 residues, 1 model selected  

> select /A-B:47

34 atoms, 32 bonds, 2 residues, 1 model selected  

> hbonds sel reveal true

10 hydrogen bonds found  

> select /A:27

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

> show sel atoms

> select clear

> select /A-B:41

28 atoms, 26 bonds, 2 residues, 1 model selected  

> select /A-B:41

28 atoms, 26 bonds, 2 residues, 1 model selected  

> hbonds sel reveal true

9 hydrogen bonds found  

> select clear

> select /A:48

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

> hide sel cartoons

> hide atoms

> show atoms

> select clear

> hide atoms

> select clear

> ~hbonds

> select clear

> select /A-B:46-47

74 atoms, 74 bonds, 4 residues, 1 model selected  

> select /A-B:46-48

114 atoms, 116 bonds, 6 residues, 1 model selected  

> select /A-B:44-45

48 atoms, 48 bonds, 4 residues, 1 model selected  

> select /A-B:44-48

162 atoms, 166 bonds, 10 residues, 1 model selected  

> show sel cartoons

> select clear

> show surfaces

> select clear

> select /A-B:61-62

70 atoms, 68 bonds, 4 residues, 1 model selected  

> select /A-B:61-62

70 atoms, 68 bonds, 4 residues, 1 model selected  

> show sel atoms

> select clear

> select /A-B:50

40 atoms, 40 bonds, 2 residues, 1 model selected  

> select /A-B:50

40 atoms, 40 bonds, 2 residues, 1 model selected  

> show sel atoms

> select clear

> transparency #2 70

> transparency #2 90

> transparency #2 80

> select clear

> save
> /Users/u6290062/Documents/PhD/Manuscripts/01_Stb6-AvrStb6/Data/1E4-dimer-
> hydrophobic.png width 791 height 739 supersample 4 transparentBackground
> true

> save
> /Users/u6290062/Documents/PhD/Manuscripts/01_Stb6-AvrStb6/Data/Fig_4_poses.cxs
> includeMaps true

> close #2

> close

> open /Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/stb6.pdb

Chain information for stb6.pdb #1  
---  
Chain | Description  
A | No description available  
  

> select ::name=""MAN""

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

> delete atoms sel

> delete bonds sel

> select ::name=""NAG""

56 atoms, 57 bonds, 4 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select clear

> save /Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/stb6-NG.pdb displayedOnly
> true relModel #1

> save /Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/stb6-NG.pdb displayedOnly
> true

> close

> open /Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/BIO-
> SAXS_data/AvrStb6_dimer_refine_027.pdb format pdb

Chain information for AvrStb6_dimer_refine_027.pdb #1  
---  
Chain | Description  
A B | No description available  
  
Computing secondary structure  

> open /Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/BIO-
> SAXS_data/AvrStb6_monomer_refine_029.pdb

Chain information for AvrStb6_monomer_refine_029.pdb #2  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> select clear

> lighting soft

> ui tool show Matchmaker

> matchmaker #2 to #1

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 AvrStb6_dimer_refine_027.pdb, chain A (#1) with
AvrStb6_monomer_refine_029.pdb, chain A (#2), sequence alignment score = 363.9  
RMSD between 57 pruned atom pairs is 0.767 angstroms; (across all 64 pairs:
1.655)  
  

> select clear

> hide atoms

> select clear

> select #1/B

880 atoms, 896 bonds, 66 residues, 1 model selected  

> hide sel cartoons

> select clear

> select add #1/A:19

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

> select add #2/A:14

14 atoms, 12 bonds, 2 residues, 2 models selected  
Alignment identifier is 1/A  
Alignment identifier is 2/A  

> select clear

> select #1/A:19

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

> select add #1/A:21

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

> select clear

> setattr #2:19-21 res ss_type 0

Assigning ss_type attribute to 3 items  

> setattr #2:19-21 res ss_type 0

Assigning ss_type attribute to 3 items  

> setattr #1:19-21 res ss_type 0

Assigning ss_type attribute to 8 items  

> setattr #2:14-16 res ss_type 0

Assigning ss_type attribute to 4 items  

> select clear

> select #1/A:32

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #1/A:33

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

> select add #1/A:36

33 atoms, 32 bonds, 2 residues, 1 model selected  

> select clear

> select #1/A:37

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select add #1/A:36

35 atoms, 35 bonds, 2 residues, 1 model selected  

> select add #1/A:35

52 atoms, 51 bonds, 3 residues, 1 model selected  

> select add #1/A:34

59 atoms, 57 bonds, 4 residues, 1 model selected  

> select add #1/A:33

71 atoms, 68 bonds, 5 residues, 1 model selected  

> select add #1/A:32

88 atoms, 84 bonds, 6 residues, 1 model selected  

> show sel atoms

> select clear

> select add #2/A:32

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select add #2/A:31

35 atoms, 35 bonds, 2 residues, 1 model selected  

> select add #2/A:30

52 atoms, 51 bonds, 3 residues, 1 model selected  

> select add #2/A:29

59 atoms, 57 bonds, 4 residues, 1 model selected  

> select add #2/A:28

71 atoms, 68 bonds, 5 residues, 1 model selected  

> select add #2/A:27

88 atoms, 84 bonds, 6 residues, 1 model selected  

> show sel atoms

> select clear

> select #2/A:32

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select #2/A:32

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select #2/A:32-36

79 atoms, 80 bonds, 5 residues, 1 model selected  

> select #2/A:28-29

19 atoms, 18 bonds, 2 residues, 1 model selected  

> select #2/A:28-32

71 atoms, 72 bonds, 5 residues, 1 model selected  

> select #2/A:23-27,32-36,51-55,59-63

271 atoms, 270 bonds, 20 residues, 1 model selected  

> select #2/A:28-29

19 atoms, 18 bonds, 2 residues, 1 model selected  

> select #2/A:28-33

95 atoms, 96 bonds, 6 residues, 1 model selected  

> select clear

> select #1/A:26

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select #1/A:26-29

47 atoms, 47 bonds, 4 residues, 1 model selected  

> select add #2/A:32

61 atoms, 61 bonds, 5 residues, 2 models selected  

> select clear

> select #1/A:20-21

23 atoms, 22 bonds, 2 residues, 1 model selected  

> select #1/A:20-26

92 atoms, 93 bonds, 7 residues, 1 model selected  

> select clear

> select #1/A:26-27

21 atoms, 21 bonds, 2 residues, 1 model selected  

> select #1/A:26-29

47 atoms, 47 bonds, 4 residues, 1 model selected  

> select clear

> select #1/A:33

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

> select #1/A:26

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select #1/A:26-33

106 atoms, 107 bonds, 8 residues, 1 model selected  

> select clear

> select #1/A:33

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

> select #1/A:33-37

71 atoms, 72 bonds, 5 residues, 1 model selected  

> select clear

> select #1/A:38-39

34 atoms, 33 bonds, 2 residues, 1 model selected  

> select #1/A:38-39

34 atoms, 33 bonds, 2 residues, 1 model selected  

> select clear

> select #1/A:28

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #1/A:28

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select clear

> select #1/A:32

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #1/A:32

17 atoms, 16 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> select #2/A:27

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #2/A:27

17 atoms, 16 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> select #1/A:32-33

29 atoms, 28 bonds, 2 residues, 1 model selected  

> select #1/A:32-37

88 atoms, 89 bonds, 6 residues, 1 model selected  

> hide sel cartoons

> select clear

> select #2/A:27-28

29 atoms, 28 bonds, 2 residues, 1 model selected  

> select #2/A:27-32

88 atoms, 89 bonds, 6 residues, 1 model selected  

> hide sel cartoons

> select clear

> select #1/A:37

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select #1/A:37

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select #2/A:33

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

> show sel atoms

> select add #1/A:38

48 atoms, 46 bonds, 2 residues, 2 models selected  

> show sel atoms

> hide sel cartoons

> select clear

> show cartoons

> hide atoms

> select clear

> select #1/B

880 atoms, 896 bonds, 66 residues, 1 model selected  

> hide sel cartoons

> select clear

> select ::name=""CYS""

360 atoms, 339 bonds, 36 residues, 2 models selected  

> show sel atoms

> select clear

> select #1/B

880 atoms, 896 bonds, 66 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> select clear

> select add #1/A:38

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

> select add #1/A:37

38 atoms, 37 bonds, 2 residues, 1 model selected  

> select #1/A:33

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

> select #1/A:33-42

146 atoms, 148 bonds, 10 residues, 1 model selected  

> show sel atoms

> select clear

> select #2/A:28

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

> select #2/A:28-37

146 atoms, 148 bonds, 10 residues, 1 model selected  

> show sel atoms

> select clear

> select #1/A:31

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

> select #1/A:31-32

37 atoms, 37 bonds, 2 residues, 1 model selected  

> show sel atoms

> select #2/A:26-27

37 atoms, 37 bonds, 2 residues, 1 model selected  

> select #2/A:26-27

37 atoms, 37 bonds, 2 residues, 1 model selected  

> show sel atoms

> select clear

> hide atoms

> close #1

> close

> open
> /Users/u6290062/Downloads/ZmWAKLYecto_58d61_0/ZmWAKLYecto_58d61_0_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb

Chain information for
ZmWAKLYecto_58d61_0_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> lighting soft

> open /Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/stb6.pdb

Chain information for stb6.pdb #2  
---  
Chain | Description  
A | No description available  
  

> close #2

> open /Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/stb6-NG.pdb

Summary of feedback from opening
/Users/u6290062/Library/CloudStorage/OneDrive-
AustralianNationalUniversity/Documents/Figures/stb6-NG.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 LEU A 80 LEU A 85 1 6  
End residue of secondary structure not found: HELIX 2 2 GLU A 126 LEU A 134 1
9  
Start residue of secondary structure not found: SHEET 1 1 1 PHE A 22 LEU A 24
0  
Start residue of secondary structure not found: SHEET 2 2 1 PHE A 41 LEU A 43
0  
Start residue of secondary structure not found: SHEET 3 3 1 THR A 44 TYR A 46
0  
Start residue of secondary structure not found: SHEET 4 4 1 TYR A 50 LEU A 53
0  
Start residue of secondary structure not found: SHEET 5 5 1 PHE A 63 SER A 69
0  
5 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (9 )  
Cannot find LINK/SSBOND residue CYS (13 )  
Cannot find LINK/SSBOND residue CYS (96 )  
Cannot find LINK/SSBOND residue CYS (124 )  
  
Chain information for stb6-NG.pdb #2  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> close #2

> open /Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/stb6.pdb

Chain information for stb6.pdb #2  
---  
Chain | Description  
A | No description available  
  

> select clear

> hide cartoons

> show cartoons

> hide atoms

> select clear

> ui tool show Matchmaker

> matchmaker #2 to #1

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
ZmWAKLYecto_58d61_0_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#1) with stb6.pdb, chain A (#2), sequence alignment score = 193.8  
RMSD between 50 pruned atom pairs is 1.179 angstroms; (across all 172 pairs:
6.786)  
  

> select add #1/A:35

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

> select add #1/A:36

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

> select add #1/A:37

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

> setattr #1:35-36 res ss_type 0

Assigning ss_type attribute to 2 items  

> select clear

Alignment identifier is 1/A  
Alignment identifier is 2/A  

> select #2/A:43

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

> select add #2/A:42

17 atoms, 15 bonds, 2 residues, 1 model selected  

> select add #2/A:41

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

> select clear

> select #1/A:37-38

21 atoms, 21 bonds, 2 residues, 1 model selected  

> select #1/A:37-39

29 atoms, 29 bonds, 3 residues, 1 model selected  

> setattr #1:37-39 res ss_type 2

Assigning ss_type attribute to 3 items  

> select #1/A:36

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

> select #1/A:36

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

> setattr #1:36-39 res ss_type 2

Assigning ss_type attribute to 4 items  

> select clear

> setattr #1:36-39 res ss_type 2

Assigning ss_type attribute to 4 items  

> setattr #1:35-39 res ss_type 2

Assigning ss_type attribute to 5 items  

> select add #1/A:23

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

> select add #1/A:26

20 atoms, 19 bonds, 2 residues, 1 model selected  

> select clear

> setattr #1:23-26 res ss_type 2

Assigning ss_type attribute to 4 items  

> select #1/A:3

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

> select #1/A:1-3

31 atoms, 32 bonds, 3 residues, 1 model selected  

> hide sel cartoons

> select clear

> select ::name=""CYS""

96 atoms, 84 bonds, 16 residues, 2 models selected  

> show sel atoms

> select clear

> bond sel

Must specify two or more atoms  

> select clear

> select add #1/A:7@SG

1 atom, 1 residue, 1 model selected  

> select add #1/A:32@SG

2 atoms, 1 bond, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select clear

> select add #1/A:13@SG

1 atom, 1 residue, 1 model selected  

> select add #1/A:41@SG

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select clear

> select add #1/A:120@SG

1 atom, 1 residue, 1 model selected  

> select add #1/A:162@SG

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select add #1/A:80@SG

3 atoms, 3 residues, 1 model selected  

> select add #1/A:135@SG

4 atoms, 4 residues, 1 model selected  

> bond sel

Created 1 bond  

> select clear

> hide #2 models

> select #1/A:206

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

> select add #1/A:205

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

> select add #1/A:204

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

> hide sel cartoons

> select clear

> select add #1/A:203

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

> select add #1/A:172

8 atoms, 6 bonds, 2 residues, 1 model selected  

> select #1/A:172

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

> select #1/A:172-202

235 atoms, 242 bonds, 31 residues, 1 model selected  

> select #1/A:205

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

> select #1/A:205-206

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

> hide sel cartoons

> select
> #1/A:23-26,35-41,46-50,53-61,66-71,113-120,130-132,141-148,162-170,194-197

535 atoms, 543 bonds, 63 residues, 1 model selected  

> select #1/A:205

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

> select #1/A:205-206

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

> select clear

> select add #1/A:203

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

> select add #1/A:202

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

> select #1/A:185-186

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

> select #1/A:185-206

169 atoms, 171 bonds, 22 residues, 1 model selected  

> select add #1/A:171

173 atoms, 174 bonds, 23 residues, 1 model selected  

> select subtract #1/A:171

169 atoms, 171 bonds, 22 residues, 1 model selected  

> select add #1/A:172

173 atoms, 174 bonds, 23 residues, 1 model selected  

> select #1/A:173-174

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

> select #1/A:173-186

104 atoms, 108 bonds, 14 residues, 1 model selected  

> select #1/A:172-173

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

> select #1/A:172-206

262 atoms, 269 bonds, 35 residues, 1 model selected  

> color sel forest green target c

> select clear

> select #1/A:154

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

> select add #1/A:155

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

> select add #1/A:156

22 atoms, 19 bonds, 3 residues, 1 model selected  

> setattr #1:154-156 res ss_type 0

Assigning ss_type attribute to 3 items  

> select clear

> select add #1/A:71

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

> select #1/A:1-2

21 atoms, 21 bonds, 2 residues, 1 model selected  

> select #1/A:1-71

560 atoms, 581 bonds, 71 residues, 1 model selected  

> color sel dark sea green target ac

> color sel light green target ac

> color sel dark sea green target ac

> select clear

> select add #1/A:113

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

> select add #1/A:110

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

> select add #1/A:112

21 atoms, 19 bonds, 3 residues, 1 model selected  

> select add #1/A:111

29 atoms, 26 bonds, 4 residues, 1 model selected  

> select subtract #1/A:113

21 atoms, 19 bonds, 3 residues, 1 model selected  

> select #1/A:72-73

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

> select #1/A:73-112

343 atoms, 357 bonds, 40 residues, 1 model selected  

> color sel light gray target ac

> select clear

> select add #1/A:72

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

> color sel light gray target ac

> select clear

> select add #1/A:171

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

> select #1/A:113

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

> select #1/A:113-171

465 atoms, 479 bonds, 59 residues, 1 model selected  

> color sel burly wood target ac

> color sel wheat target ac

> color sel goldenrod target ac

> color sel dark khaki target ac

> select clear

> select add #1/A:122

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

> select add #1/A:123

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select add #1/A:124

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

> select add #1/A:125

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

> select add #1/A:126

41 atoms, 37 bonds, 5 residues, 1 model selected  

> select add #1/A:127

49 atoms, 44 bonds, 6 residues, 1 model selected  

> select add #1/A:121

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

> setattr #1:121-127 res ss_type 1

Assigning ss_type attribute to 7 items  

> select clear

> setattr #1:121-127 res ss_type 0

Assigning ss_type attribute to 7 items  

> select ::name=""CYS""

96 atoms, 88 bonds, 16 residues, 2 models selected  

> color (#1 & sel) byhetero

> select clear

> select #1/A:4-5

20 atoms, 21 bonds, 2 residues, 1 model selected  

> select #1/A:4-5

20 atoms, 21 bonds, 2 residues, 1 model selected  

> select #1/A:5

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

> select #1/A:5-6

17 atoms, 17 bonds, 2 residues, 1 model selected  

> select #1/A:4

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

> select #1/A:4-6

27 atoms, 28 bonds, 3 residues, 1 model selected  

> select #1/A:5

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

> select #1/A:4-5

20 atoms, 21 bonds, 2 residues, 1 model selected  

> hide sel cartoons

> select clear

> lighting soft

> select ::name=""ASN""

168 atoms, 149 bonds, 21 residues, 2 models selected  

> select clear

> select add #1/A:138

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

> select add #1/A:119

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

> select add #1/A:95

24 atoms, 21 bonds, 3 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> select clear

> select #1/A:72

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

> select add #1/A:111

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

> select add #1/A:112

19 atoms, 16 bonds, 3 residues, 1 model selected  

> select #1/A:72-73

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

> select #1/A:73-113

351 atoms, 365 bonds, 41 residues, 1 model selected  

> select #1/A:112

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

> select #1/A:111-112

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

> select #1/A:72

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

> select #1/A:72-112

348 atoms, 362 bonds, 41 residues, 1 model selected  

> color sel honeydew target ac

> color sel white smoke target ac

> select clear

> select #1/A:72

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

> select #1/A:72-112

348 atoms, 362 bonds, 41 residues, 1 model selected  

> color sel light gray target ac

> select clear

> select ::name=""ASN""

168 atoms, 149 bonds, 21 residues, 2 models selected  

> color (#1 & sel) byhetero

> select clear

> select add #1/A:80

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

> color sel byhetero

> select clear

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/ZmWAKL-Y.png""
> width 900 height 739 supersample 4 transparentBackground true

> select clear

> hide #1 models

> open
> /Users/u6290062/Downloads/ZmWAK_b7dcf/ZmWAK_b7dcf_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb

Chain information for
ZmWAK_b7dcf_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb #3  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> select clear

> ui tool show Matchmaker

> matchmaker #2 to #3

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 ZmWAK_b7dcf_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb,
chain A (#3) with stb6.pdb, chain A (#2), sequence alignment score = 106.7  
RMSD between 44 pruned atom pairs is 1.034 angstroms; (across all 159 pairs:
16.006)  
  

> show #2 models

Alignment identifier is 1/A  
Destroying pre-existing alignment with identifier 2/A  
Alignment identifier is 2/A  
Alignment identifier is 3/A  

> select #2/A:41

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

> select #2/A:41-46

53 atoms, 54 bonds, 6 residues, 1 model selected  

> select clear

Drag select of 3 residues  

> select clear

> select add #3/A:19

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

> select add #3/A:21

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select #3/A:19

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

> select #3/A:19-21

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

> setattr #3:19-21 res ss_type 2

Assigning ss_type attribute to 3 items  

> select clear

> select add #3/A:29

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

> select add #2/A:41

15 atoms, 14 bonds, 2 residues, 2 models selected  

> select subtract #2/A:41

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

> select add #3/A:30

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

> select add #3/A:31

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

> select add #3/A:28

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

> setattr #3:28-31 res ss_type 2

Assigning ss_type attribute to 4 items  

> setattr #3:28-30 res ss_type 2

Assigning ss_type attribute to 3 items  

> setattr #3:28-30 res ss_type 0

Assigning ss_type attribute to 3 items  

> setattr #3:28-30 res ss_type 2

Assigning ss_type attribute to 3 items  

> select clear

> hide #2 models

> select clear

> select ::name=""CYS""

240 atoms, 209 bonds, 40 residues, 3 models selected  

> color (#3 & sel) byhetero

> show sel & #3 atoms

> select clear

> select add #3/A:5

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

> select #3/A:1

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

> select #3/A:1-4

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

> hide sel cartoons

> select clear

> select add #3/A:6@SG

1 atom, 1 residue, 1 model selected  

> select add #3/A:25@SG

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select clear

> select add #3/A:10@SG

1 atom, 1 residue, 1 model selected  

> select add #3/A:34@SG

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select add #3/A:324@SG

3 atoms, 3 residues, 1 model selected  

> select add #3/A:333@SG

4 atoms, 4 residues, 1 model selected  

> bond sel

Created 1 bond  

> select add #3/A:322@SG

5 atoms, 5 residues, 1 model selected  

> select add #3/A:307@SG

6 atoms, 6 residues, 1 model selected  

> bond sel

Created 1 bond  

> select add #3/A:313@SG

7 atoms, 7 residues, 1 model selected  

> select add #3/A:299@SG

8 atoms, 8 residues, 1 model selected  

> bond sel

Created 1 bond  

> select add #3/A:293@SG

9 atoms, 9 residues, 1 model selected  

> select add #3/A:277@SG

10 atoms, 10 residues, 1 model selected  

> bond sel

Created 1 bond  

> select add #3/A:257@SG

11 atoms, 11 residues, 1 model selected  

> select add #3/A:275@SG

12 atoms, 12 residues, 1 model selected  

> bond sel

Created 1 bond  

> select add #3/A:264@SG

13 atoms, 13 residues, 1 model selected  

> select add #3/A:246@SG

14 atoms, 14 residues, 1 model selected  

> bond sel

Created 1 bond  

> select add #3/A:189@SG

15 atoms, 15 residues, 1 model selected  

> select add #3/A:115@SG

16 atoms, 16 residues, 1 model selected  

> bond sel

Created 1 bond  

> select add #3/A:156@SG

17 atoms, 17 residues, 1 model selected  

> select add #3/A:161@SG

18 atoms, 18 residues, 1 model selected  

> bond sel

Created 1 bond  

> select add #3/A:162@SG

19 atoms, 19 residues, 1 model selected  

> select add #3/A:141@SG

20 atoms, 20 residues, 1 model selected  

> bond sel

Created 1 bond  

> select clear

> select add #3/A:78@SG

1 atom, 1 residue, 1 model selected  

> select add #3/A:191@SG

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select clear

> select add #3/A:251

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

> select add #3/A:250

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

> select add #3/A:249

20 atoms, 18 bonds, 3 residues, 1 model selected  

> setattr #3/A:249-251 res ss_type 2

Assigning ss_type attribute to 3 items  

> setattr #3/A:249-251 res ss_type 0

Assigning ss_type attribute to 3 items  

> select clear

> select add #3/A:300

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

> select add #3/A:299

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

> select add #3/A:298

24 atoms, 21 bonds, 3 residues, 1 model selected  

> setattr #3/A:298-300 res ss_type 0

Assigning ss_type attribute to 3 items  

> select clear

> select add #3/A:209

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

> select add #3/A:208

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

> select add #3/A:207

22 atoms, 19 bonds, 3 residues, 1 model selected  

> select add #3/A:206

27 atoms, 23 bonds, 4 residues, 1 model selected  

> setattr #3/A:206-209 res ss_type 0

Assigning ss_type attribute to 4 items  

> select clear

> select add #3/A:302

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

> select add #3/A:303

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select add #3/A:304

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

> setattr #3/A:302-304 res ss_type 0

Assigning ss_type attribute to 3 items  

> select clear

> select add #3/A:219

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

> select add #3/A:220

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

> select add #3/A:221

23 atoms, 21 bonds, 3 residues, 1 model selected  

> setattr #3/A:219-221 res ss_type 0

Assigning ss_type attribute to 3 items  

> select clear

> select add #3/A:214

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

> select add #3/A:204

18 atoms, 18 bonds, 2 residues, 1 model selected  

> setattr #3/A:204-214 res ss_type 1

Assigning ss_type attribute to 11 items  

> select clear

> select add #3/A:204

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

> select add #3/A:205

20 atoms, 19 bonds, 2 residues, 1 model selected  

> setattr #3/A:sel res ss_type 1

Assigning ss_type attribute to 0 items  

> select clear

> select add #3/A:204

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

> select add #3/A:205

20 atoms, 19 bonds, 2 residues, 1 model selected  

> setattr #3/A:204-205 res ss_type 1

Assigning ss_type attribute to 2 items  

> setattr #3/A:204-205 res ss_type 0

Assigning ss_type attribute to 2 items  

> select clear

> select add #3/A:214

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

> select add #3/A:213

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

> setattr #3/A:213-214 res ss_type 0

Assigning ss_type attribute to 2 items  

> select clear

> select add #3/A:236

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

> select add #3/A:237

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

> select add #3/A:238

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

> select clear

> select add #3/A:199

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

> select add #3/A:200

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

> select subtract #3/A:199

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

> select add #3/A:232

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

> select #3/A:200

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

> select #3/A:200-233

285 atoms, 296 bonds, 34 residues, 1 model selected  

> color sel forest green target ac

> select clear

> select #3/A:234

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

> select #3/A:234-339

801 atoms, 825 bonds, 106 residues, 1 model selected  

> color sel pink target ac

> color sel dark turquoise target ac

> color sel light sea green target ac

> color sel teal target ac

> color sel yellow green target ac

> color sel sandy brown target ac

> color sel royal blue target ac

> select clear

> select #3/A:73

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

> select #3/A:74

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

> select #3/A:75

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

> select #3/A:74

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

> select #3/A:73

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

> select #3/A:1

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

> select #3/A:1-73

543 atoms, 556 bonds, 73 residues, 1 model selected  

> color sel dark sea green target ac

> select clear

> select add #3/A:199

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

> select add #3/A:74

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

> select #3/A:74-75

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

> select #3/A:74-199

971 atoms, 1000 bonds, 126 residues, 1 model selected  

> color sel dark khaki target ac

> select clear

> select add #3/A:234

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

> select #3/A:234

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

> select #3/A:234-339

801 atoms, 825 bonds, 106 residues, 1 model selected  

> color sel dim gray target ac

> color sel lavender target ac

> color sel pale goldenrod target ac

> color sel khaki target ac

> color sel wheat target ac

> color sel light steel blue target ac

> color sel powder blue target ac

> color sel light blue target ac

> color sel light steel blue target ac

> select clear

> select ::name=""CYS""

240 atoms, 221 bonds, 40 residues, 3 models selected  

> color (#3 & sel) byhetero

> select clear

> select add #3/A:334

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

> select #3/A:334

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

> select #3/A:334-339

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

> hide sel cartoons

> select clear

> select add #3/A:74

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

> select add #3/A:108

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

> select subtract #3/A:108

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

> select add #3/A:107

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

> select #3/A:74

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

> select #3/A:74-107

256 atoms, 262 bonds, 34 residues, 1 model selected  

> color sel light gray target ac

> select clear

> select ::name=""CYS""

240 atoms, 221 bonds, 40 residues, 3 models selected  

> color (#3 & sel) byhetero

> select clear

> select add #3/A:208

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

> select add #3/A:207

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

> select add #3/A:209

22 atoms, 19 bonds, 3 residues, 1 model selected  

> setattr #3/A:207-209 res ss_type 0

Assigning ss_type attribute to 3 items  

> select clear

> select add #3/A:212

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

> select add #3/A:211

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select add #3/A:213

23 atoms, 21 bonds, 3 residues, 1 model selected  

> select add #3/A:210

30 atoms, 27 bonds, 4 residues, 1 model selected  

> setattr #3/A:210-213 res ss_type 0

Assigning ss_type attribute to 4 items  

> select clear

> select ::name=""ASN""

352 atoms, 311 bonds, 44 residues, 3 models selected  

> select clear

> show #1 models

> hide #1 models

> select clear

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/ZmWAK.png""
> width 900 height 739 supersample 4 transparentBackground true

> select clear

> hide #3 models

> open
> /Users/u6290062/Downloads/Xa4_7f217/Xa4_7f217_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb

Chain information for
Xa4_7f217_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #4  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  
Alignment identifier is 1/A  
Destroying pre-existing alignment with identifier 2/A  
Alignment identifier is 2/A  
Destroying pre-existing alignment with identifier 3/A  
Alignment identifier is 3/A  
Alignment identifier is 4/A  

> select #4/A:26

8 atoms, 7 bonds, 1 residue, 1 model selected  
Drag select of 4 residues  

> select clear

> select add #4/A:27

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

> select add #4/A:25

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

> setattr #3/A:25-27 res ss_type 0

Assigning ss_type attribute to 3 items  

> setattr #4/A:25-27 res ss_type 0

Assigning ss_type attribute to 3 items  

> select clear

> show #2 models

> ui tool show Matchmaker

> matchmaker #2 to #4

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 Xa4_7f217_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#4) with stb6.pdb, chain A (#2), sequence alignment score = 103.2  
RMSD between 47 pruned atom pairs is 0.921 angstroms; (across all 161 pairs:
14.144)  
  

> select add #4/A:34

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

> select add #4/A:37

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

> select #4/A:35

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

> select #4/A:35-37

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

> setattr #4/A:35-37 res ss_type 2

Assigning ss_type attribute to 3 items  

> select clear

> select add #4/A:22

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

> select add #4/A:24

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select add #4/A:25

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

> setattr #4/A:22-25 res ss_type 2

Assigning ss_type attribute to 4 items  

> select clear

> hide #2 models

> select clear

> select ::name=""CYS""

384 atoms, 342 bonds, 64 residues, 4 models selected  

> show sel & #4 atoms

> select clear

> select add #4/A:9@SG

1 atom, 1 residue, 1 model selected  

> select add #4/A:27@SG

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select clear

> select add #4/A:13@SG

1 atom, 1 residue, 1 model selected  

> select add #4/A:39@SG

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select #4/A:180@SG

1 atom, 1 residue, 1 model selected  

> select add #4/A:71@SG

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select clear

> select add #4/A:131@SG

1 atom, 1 residue, 1 model selected  

> select add #4/A:109@SG

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select add #4/A:150@SG

3 atoms, 3 residues, 1 model selected  

> select add #4/A:127@SG

4 atoms, 4 residues, 1 model selected  

> bond sel

Created 1 bond  

> select add #4/A:144@SG

5 atoms, 5 residues, 1 model selected  

> select add #4/A:149@SG

6 atoms, 6 residues, 1 model selected  

> bond sel

Created 1 bond  

> select clear

> select add #4/A:245@SG

1 atom, 1 residue, 1 model selected  

> select add #4/A:228@SG

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select add #4/A:256@SG

3 atoms, 3 residues, 1 model selected  

> select add #4/A:238@SG

4 atoms, 4 residues, 1 model selected  

> bond sel

Created 1 bond  

> select add #4/A:258@SG

5 atoms, 5 residues, 1 model selected  

> select add #4/A:272@SG

6 atoms, 6 residues, 1 model selected  

> bond sel

Created 1 bond  

> select add #4/A:291@SG

7 atoms, 7 residues, 1 model selected  

> select add #4/A:278@SG

8 atoms, 8 residues, 1 model selected  

> bond sel

Created 1 bond  

> select add #4/A:300@SG

9 atoms, 9 residues, 1 model selected  

> select add #4/A:285@SG

10 atoms, 10 residues, 1 model selected  

> bond sel

Created 1 bond  

> select add #4/A:320@SG

11 atoms, 11 residues, 1 model selected  

> select add #4/A:302@SG

12 atoms, 12 residues, 1 model selected  

> bond sel

Created 1 bond  

> select clear

> select add #4/A:8

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

> select #4/A:6

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

> select #4/A:1-6

43 atoms, 44 bonds, 6 residues, 1 model selected  

> hide sel cartoons

> select clear

> select add #4/A:325

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

> select add #4/A:322

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

> select add #4/A:321

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

> select #4/A:321-322

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

> select #4/A:321-326

44 atoms, 45 bonds, 6 residues, 1 model selected  

> hide sel cartoons

> select clear

> select add #4/A:135

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

> select add #4/A:136

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

> select add #4/A:134

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

> setattr #4:134-136 res ss_type 0

Assigning ss_type attribute to 3 items  

> select clear

> select add #4/A:198

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

> select add #4/A:195

22 atoms, 21 bonds, 2 residues, 1 model selected  

> setattr #4:195-198 res ss_type 0

Assigning ss_type attribute to 4 items  

> select clear

> select add #4/A:188

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

> select add #4/A:189

19 atoms, 18 bonds, 2 residues, 1 model selected  

> select subtract #4/A:188

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

> select add #4/A:221

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

> select #4/A:189

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

> select #4/A:189-221

294 atoms, 304 bonds, 33 residues, 1 model selected  

> color sel forest green target ac

> select clear

> select add #4/A:222

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

> select #4/A:222-224

28 atoms, 27 bonds, 3 residues, 1 model selected  

> select #4/A:222-326

777 atoms, 796 bonds, 105 residues, 1 model selected  

> color sel light steel blue target ac

> select clear

> select add #4/A:67

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

> select add #4/A:101

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

> select #4/A:67-68

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

> select #4/A:67-101

276 atoms, 281 bonds, 35 residues, 1 model selected  

> color sel light gray target ac

> select clear

> select add #4/A:66

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

> select #4/A:1

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

> select #4/A:1-66

505 atoms, 524 bonds, 66 residues, 1 model selected  

> color sel dark sea green target ac

> select clear

> select add #4/A:102

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

> select add #4/A:188

17 atoms, 15 bonds, 2 residues, 1 model selected  

> select #4/A:102

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

> select #4/A:102-188

628 atoms, 644 bonds, 87 residues, 1 model selected  

> color sel dark khaki target ac

> select clear

> select ::name=""CYS""

384 atoms, 354 bonds, 64 residues, 4 models selected  

> color (#4 & sel) byhetero

> select clear

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Xa4.png"" width
> 900 height 739 supersample 4 transparentBackground true

> hide #4 models

> open
> /Users/u6290062/Downloads/snn1_d97b8/snn1_d97b8_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb

Chain information for
snn1_d97b8_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #5  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> select clear

> hide #5 models

> show #4 models

> color bfactor palette
> 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue

10982 atoms, 1423 residues, atom bfactor range 32.5 to 191  

> select clear

> hide #4 atoms

> select clear

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Xa4-pLDDT.png""
> width 900 height 739 supersample 4 transparentBackground true

> select clear

> hide #4 models

> show #3 models

> hide #3 atoms

> select clear

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/ZmWAK-
> pLDDT.png"" width 900 height 739 supersample 4 transparentBackground true

> select clear

> hide #3 models

> show #1 models

> select clear

> hide #1 atoms

> select clear

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/ZmWAKL-Y-
> pLDDT.png"" width 900 height 739 supersample 4 transparentBackground true

> hide #1 models

> show #5 models

> color #5 #d4fb79ff

> show #2 models

> ui tool show Matchmaker

> matchmaker #2 to #5

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 snn1_d97b8_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#5) with stb6.pdb, chain A (#2), sequence alignment score = 78.7  
RMSD between 44 pruned atom pairs is 0.933 angstroms; (across all 166 pairs:
14.577)  
  

> color #5 #941751ff

> color #5 #ff2f92ff

> color #5 #ff8ad8ff

> color #5 #ff85ffff

> color #5 #73fcd6ff

> color #5 #ff8ad8ff

> select clear

> color #2 #d6d6d6ff

> select clear

> select add #5/A:31

11 atoms, 11 bonds, 1 residue, 1 model selected  
Alignment identifier is 5/A  

> select #5/A:31

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

> select #5/A:31-36

48 atoms, 48 bonds, 6 residues, 1 model selected  

> setattr #5:31-36 res ss_type 2

Assigning ss_type attribute to 6 items  

> select clear

> setattr #5:30-36 res ss_type 2

Assigning ss_type attribute to 7 items  

> setattr #5:29-36 res ss_type 2

Assigning ss_type attribute to 8 items  

> setattr #5:29-36 res ss_type 0

Assigning ss_type attribute to 8 items  

> setattr #5:30-36 res ss_type 2

Assigning ss_type attribute to 7 items  

> select clear

> select add #5/A:20

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

> select #5/A:21

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

> select #5/A:21-22

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

> select #5/A:20

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

> select #5/A:20-22

23 atoms, 23 bonds, 3 residues, 1 model selected  

> setattr #5:20-22 res ss_type 2

Assigning ss_type attribute to 3 items  

> select clear

> hide #2 models

> select clear

> select ::name=""CYS""

516 atoms, 465 bonds, 86 residues, 5 models selected  

> show sel & #5 atoms

> color (#5 & sel) byhetero

> select clear

> select #5/A:7@SG

1 atom, 1 residue, 1 model selected  

> select add #5/A:26@SG

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select #5/A:11@SG

1 atom, 1 residue, 1 model selected  

> select add #5/A:35@SG

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select add #5/A:208@SG

3 atoms, 3 residues, 1 model selected  

> select add #5/A:94@SG

4 atoms, 4 residues, 1 model selected  

> bond sel

Created 1 bond  

> select add #5/A:170@SG

5 atoms, 5 residues, 1 model selected  

> select add #5/A:175@SG

6 atoms, 6 residues, 1 model selected  

> bond sel

Created 1 bond  

> select add #5/A:152@SG

7 atoms, 7 residues, 1 model selected  

> select add #5/A:176@SG

8 atoms, 8 residues, 1 model selected  

> select subtract #5/A:176@SG

7 atoms, 7 residues, 1 model selected  

> select add #5/A:176@SG

8 atoms, 8 residues, 1 model selected  

> bond sel

Created 0 bonds  

> bond sel

Created 0 bonds  

> select clear

> select add #5/A:152@SG

1 atom, 1 residue, 1 model selected  

> select add #5/A:176@SG

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 0 bonds  

> select clear

> select add #5/A:152@SG

1 atom, 1 residue, 1 model selected  

> select add #5/A:176@SG

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 0 bonds  

> select clear

> select add #5/A:210

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

> select clear

> select add #5/A:176@SG

1 atom, 1 residue, 1 model selected  

> select add #5/A:152@SG

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 0 bonds  

> select clear

> select add #5/A:331@SG

1 atom, 1 residue, 1 model selected  

> select add #5/A:344@SG

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select add #5/A:329@SG

3 atoms, 3 residues, 1 model selected  

> select add #5/A:314@SG

4 atoms, 4 residues, 1 model selected  

> bond sel

Created 1 bond  

> select add #5/A:306@SG

5 atoms, 5 residues, 1 model selected  

> select add #5/A:320@SG

6 atoms, 6 residues, 1 model selected  

> bond sel

Created 1 bond  

> select clear

> select add #5/A:266@SG

1 atom, 1 residue, 1 model selected  

> select add #5/A:284@SG

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select clear

> select add #5/A:300@SG

1 atom, 1 residue, 1 model selected  

> select add #5/A:286@SG

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select clear

> select add #5/A:273@SG

1 atom, 1 residue, 1 model selected  

> select add #5/A:253@SG

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select clear

> select add #5/A:6

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

> select #5/A:1

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

> select #5/A:1-4

32 atoms, 31 bonds, 4 residues, 1 model selected  

> select #5/A:1

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

> select #5/A:1-5

41 atoms, 40 bonds, 5 residues, 1 model selected  

> hide sel cartoons

> select clear

> select add #5/A:238

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

> select add #5/A:235

22 atoms, 20 bonds, 2 residues, 1 model selected  

> setattr #4:235-238 res ss_type 2

Assigning ss_type attribute to 4 items  

> setattr #5:235-238 res ss_type 1

Assigning ss_type attribute to 4 items  

> select clear

> select add #5/A:247

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

> select add #5/A:216

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

> select #5/A:216

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

> select #5/A:216-247

266 atoms, 274 bonds, 32 residues, 1 model selected  

> color sel forest green target ac

> select clear

> select add #5/A:73

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

> select add #5/A:71

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

> select add #5/A:72

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

> setattr #5:71-73 res ss_type 0

Assigning ss_type attribute to 3 items  

> select clear

> select add #5/A:74

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

> select add #5/A:121

19 atoms, 17 bonds, 2 residues, 1 model selected  

> select #5/A:74

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

> select #5/A:74-125

396 atoms, 404 bonds, 52 residues, 1 model selected  

> select #5/A:120

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

> select #5/A:120-121

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select #5/A:120-121

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select #5/A:74

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

> select #5/A:74-121

365 atoms, 373 bonds, 48 residues, 1 model selected  

> color sel light gray target ac

> select clear

> select add #5/A:73

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

> select #5/A:1-2

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

> select #5/A:1-73

564 atoms, 582 bonds, 73 residues, 1 model selected  

> color sel dark sea green target ac

> select clear

> select #5/A:248

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

> select #5/A:249

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

> select #5/A:249-346

713 atoms, 741 bonds, 98 residues, 1 model selected  

> color sel light steel blue target ac

> select clear

> select add #5/A:248

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

> color sel light steel blue target ac

> select clear

> select add #5/A:122

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

> select add #5/A:215

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

> select #5/A:122-123

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #5/A:122-215

732 atoms, 755 bonds, 94 residues, 1 model selected  

> color sel dark khaki target ac

> select clear

> select ::name=""CYS""

516 atoms, 475 bonds, 86 residues, 5 models selected  

> show sel & #5 atoms

> color (#5 & sel) byhetero

> select clear

> select add #5/A:225

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

> select add #5/A:226

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

> setattr #5:225-226 res ss_type 0

Assigning ss_type attribute to 2 items  

> select clear

> select add #5/A:224

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

> select add #5/A:223

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

> setattr #5:223-224 res ss_type 0

Assigning ss_type attribute to 2 items  

> select clear

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Snn1.png"" width
> 900 height 739 supersample 4 transparentBackground true

> color bfactor palette
> 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue

10982 atoms, 1423 residues, atom bfactor range 32.5 to 191  

> select clear

> hide #5 atoms

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Snn1-pLDDT.png""
> width 900 height 739 supersample 4 transparentBackground true

> hide #5 models

> open
> /Users/u6290062/Downloads/rlm9_d87e1/rlm9_d87e1_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb

Chain information for
rlm9_d87e1_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb #6  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> open
> /Users/u6290062/Downloads/rlm4_42bc7/rlm4_42bc7_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb

Chain information for
rlm4_42bc7_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #7  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> open
> /Users/u6290062/Downloads/rlm7_404af/rlm7_404af_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb

Chain information for
rlm7_404af_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #8  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> hide #6 models

> hide #7 models

> hide #8 models

> show #7 models

> hide #7 models

> show #6 models

> color bfactor palette
> 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue

18945 atoms, 2467 residues, atom bfactor range 32.5 to 191  

> hide #6 models

> show #7 models

> hide #7 models

> show #8 models

> hide #8 models

> show #6 models

> select clear

> color #7 white

> close #7

> close #8

> color #6 white

> select clear

> show #2 models

> color #2 #00fdffff

> select clear

> ui tool show Matchmaker

> matchmaker #2 to #6

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 rlm9_d87e1_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#6) with stb6.pdb, chain A (#2), sequence alignment score = 83.2  
RMSD between 26 pruned atom pairs is 0.902 angstroms; (across all 150 pairs:
20.495)  
  

> select add #6/A:16

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

> select add #6/A:18

19 atoms, 18 bonds, 2 residues, 1 model selected  
Alignment identifier is 6/A  

> select #6/A:16-17

15 atoms, 15 bonds, 2 residues, 1 model selected  

> select #6/A:16-18

23 atoms, 23 bonds, 3 residues, 1 model selected  

> setattr #6:16-18 res ss_type 2

Assigning ss_type attribute to 3 items  

> select clear

> select add #6/A:26

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

> select add #6/A:28

21 atoms, 20 bonds, 2 residues, 1 model selected  

> setattr #6:26-28 res ss_type 0

Assigning ss_type attribute to 3 items  

> select #6/A:32

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

> select add #6/A:30

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

> select add #6/A:27

28 atoms, 27 bonds, 3 residues, 1 model selected  

> setattr #6:27-30 res ss_type 2

Assigning ss_type attribute to 4 items  

> select clear

> hide #2 models

> select clear

> select ::name=""CYS""

660 atoms, 596 bonds, 110 residues, 6 models selected  

> show sel & #6 atoms

> color (#6 & sel) byhetero

> select clear

> select #6/A:3@SG

1 atom, 1 residue, 1 model selected  

> select add #6/A:22@SG

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select add #6/A:7@SG

3 atoms, 3 residues, 1 model selected  

> select add #6/A:32@SG

4 atoms, 4 residues, 1 model selected  

> bond sel

Created 1 bond  

> select add #6/A:213@SG

5 atoms, 5 residues, 1 model selected  

> select add #6/A:88@SG

6 atoms, 6 residues, 1 model selected  

> bond sel

Created 1 bond  

> select add #6/A:139@SG

7 atoms, 7 residues, 1 model selected  

> select add #6/A:119@SG

8 atoms, 8 residues, 1 model selected  

> bond sel

Created 1 bond  

> select add #6/A:140

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

> select add #6/A:187@SG

17 atoms, 7 bonds, 10 residues, 1 model selected  

> bond sel

Created 0 bonds  

> select clear

> select add #6/A:135@SG

1 atom, 1 residue, 1 model selected  

> select add #6/A:187@SG

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select clear

> select add #6/A:186@SG

1 atom, 1 residue, 1 model selected  

> select add #6/A:181@SG

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select add #6/A:170@SG

3 atoms, 3 residues, 1 model selected  

> select clear

> select add #6/A:170@SG

1 atom, 1 residue, 1 model selected  

> select add #6/A:156@SG

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select clear

> select add #6/A:288@SG

1 atom, 1 residue, 1 model selected  

> select add #6/A:300@SG

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select clear

> select add #6/A:316@SG

1 atom, 1 residue, 1 model selected  

> select add #6/A:302@SG

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select clear

> select add #6/A:286@SG

1 atom, 1 residue, 1 model selected  

> select add #6/A:263@SG

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select clear

> select add #6/A:345@SG

1 atom, 1 residue, 1 model selected  

> select clear

> select add #6/A:345@SG

1 atom, 1 residue, 1 model selected  

> select add #6/A:331@SG

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select clear

> select add #6/A:336@SG

1 atom, 1 residue, 1 model selected  

> select add #6/A:322@SG

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select clear

> select add #6/A:83

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

> select add #6/A:82

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

> select subtract #6/A:83

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

> select add #6/A:1

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select #6/A:82

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

> select #6/A:1-82

635 atoms, 655 bonds, 82 residues, 1 model selected  

> color sel dark sea green target ac

> select clear

> select add #6/A:247

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select add #6/A:248

25 atoms, 26 bonds, 2 residues, 1 model selected  

> select add #6/A:220

33 atoms, 33 bonds, 3 residues, 1 model selected  

> select #6/A:220

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

> select #6/A:220-263

348 atoms, 355 bonds, 44 residues, 1 model selected  

> select #6/A:248

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

> select #6/A:248

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

> select #6/A:248

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

> select #6/A:220-248

231 atoms, 236 bonds, 29 residues, 1 model selected  

> color sel forest green target ac

> select clear

> select add #6/A:249

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

> select #6/A:250

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

> select #6/A:250-350

793 atoms, 818 bonds, 101 residues, 1 model selected  

> select #6/A:249

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

> select #6/A:249-350

801 atoms, 826 bonds, 102 residues, 1 model selected  

> color sel light steel blue target ac

> select clear

> select add #6/A:219

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

> select add #6/A:113

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

> select #6/A:219

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

> select #6/A:113-219

808 atoms, 823 bonds, 107 residues, 1 model selected  

> color sel dark khaki target ac

> select clear

> select ::name=""CYS""

660 atoms, 608 bonds, 110 residues, 6 models selected  

> color (#6 & sel) byhetero

> select clear

> select add #6/A:88

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

> color sel byhetero

> select clear

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Rlm9.png"" width
> 900 height 739 supersample 4 transparentBackground true

> select clear

> color bfactor palette
> 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue

13680 atoms, 1773 residues, atom bfactor range 32.5 to 191  

> select clear

> hide #6 atoms

> select clear

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Rlm9-pLDDT.png""
> width 900 height 739 supersample 4 transparentBackground true

> hide #6 models

> open
> /Users/u6290062/Downloads/Htn1_00234/Htn1_00234_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb

Chain information for
Htn1_00234_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #7  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> color #7 white

> select clear

> select #7/A:20

8 atoms, 7 bonds, 1 residue, 1 model selected  
Alignment identifier is 7/A  

> select #7/A:20

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

> select #7/A:1-20

148 atoms, 156 bonds, 20 residues, 1 model selected  

> hide sel cartoons

> select clear

> color #2 #8efa00ff

> show #2 models

> select clear

> ui tool show Matchmaker

> matchmaker #2 to #7

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 Htn1_00234_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#7) with stb6.pdb, chain A (#2), sequence alignment score = 103.3  
RMSD between 69 pruned atom pairs is 0.971 angstroms; (across all 182 pairs:
9.215)  
  

> select add #7/A:64

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

> select add #7/A:63

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

> select add #7/A:62

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

> setattr #7:62-64 res ss_type 2

Assigning ss_type attribute to 3 items  

> select clear

> select add #7/A:45

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

> select add #7/A:43

19 atoms, 18 bonds, 2 residues, 1 model selected  

> setattr #7:43-45 res ss_type 2

Assigning ss_type attribute to 3 items  

> select clear

> hide #2 models

> select ::name=""CYS""

744 atoms, 678 bonds, 124 residues, 7 models selected  

> show sel & #7 atoms

> color (#7 & sel) byhetero

> select clear

> select add #7/A:281@SG

1 atom, 1 residue, 1 model selected  

> select add #7/A:271@SG

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select add #7/A:269@SG

3 atoms, 3 residues, 1 model selected  

> select add #7/A:249@SG

4 atoms, 4 residues, 1 model selected  

> select add #7/A:258@SG

5 atoms, 5 residues, 1 model selected  

> select add #7/A:246@SG

6 atoms, 6 residues, 1 model selected  

> select add #7/A:29@SG

7 atoms, 7 residues, 1 model selected  

> select add #7/A:59@SG

8 atoms, 8 residues, 1 model selected  

> bond sel

Created 3 bonds  

> select clear

> select add #7/A:34@SG

1 atom, 1 residue, 1 model selected  

> select add #7/A:68@SG

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select add #7/A:281

8 atoms, 5 bonds, 3 residues, 1 model selected  

> select #7/A:31

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

> select #7/A:1-31

225 atoms, 235 bonds, 31 residues, 1 model selected  

> hide sel cartoons

> select clear

> select #7/A:31

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

> select #7/A:1-31

225 atoms, 235 bonds, 31 residues, 1 model selected  

> show sel cartoons

> select clear

> select add #7/A:26

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

> select add #7/A:27

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

> select add #7/A:28

19 atoms, 16 bonds, 3 residues, 1 model selected  

> select add #7/A:29

25 atoms, 21 bonds, 4 residues, 1 model selected  

> select clear

> select add #7/A:199@SG

1 atom, 1 residue, 1 model selected  

> select add #7/A:148@SG

2 atoms, 2 residues, 1 model selected  

> select add #7/A:117@SG

3 atoms, 1 bond, 3 residues, 1 model selected  

> bond sel

Created 1 bond  

> select clear

> select #7/A:117@SG

1 atom, 1 residue, 1 model selected  

> select add #7/A:166@SG

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select clear

> select add #7/A:26

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

> select add #7/A:28

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

> select add #7/A:29

19 atoms, 16 bonds, 3 residues, 1 model selected  

> setattr #2/A:26-29 res ss_type 0

Assigning ss_type attribute to 4 items  

> setattr #7:26-29 res ss_type 0

Assigning ss_type attribute to 4 items  

> select clear

> select add #7/A:1

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

> select add #7/A:27

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #7/A:27

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

> select #7/A:1-27

199 atoms, 209 bonds, 27 residues, 1 model selected  

> hide sel cartoons

> select clear

> select add #7/A:282

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

> select add #7/A:291

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

> select #7/A:282-283

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

> select #7/A:282-291

81 atoms, 81 bonds, 10 residues, 1 model selected  

> hide sel cartoons

> select clear

> select add #7/A:86

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

> select #7/A:86

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

> select #7/A:1-86

655 atoms, 682 bonds, 86 residues, 1 model selected  

> color sel dark sea green target ac

> select clear

> select add #7/A:208

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

> select add #7/A:238

25 atoms, 25 bonds, 2 residues, 1 model selected  

> select #7/A:208

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

> select #7/A:208-238

256 atoms, 260 bonds, 31 residues, 1 model selected  

> color sel forest green target ac

> select clear

> select add #7/A:239

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

> select #7/A:239

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

> select #7/A:239-291

391 atoms, 400 bonds, 53 residues, 1 model selected  

> color sel light steel blue target ac

> select clear

> select add #7/A:208

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

> select add #7/A:139

22 atoms, 21 bonds, 2 residues, 1 model selected  

> select #7/A:139-140

19 atoms, 19 bonds, 2 residues, 1 model selected  

> select #7/A:139-208

558 atoms, 577 bonds, 70 residues, 1 model selected  

> color sel dark khaki target ac

> select clear

> select ::name=""CYS""

744 atoms, 685 bonds, 124 residues, 7 models selected  

> color (#7 & sel) byhetero

> select clear

> select ::name=""ASN""

1000 atoms, 881 bonds, 125 residues, 7 models selected  

> select clear

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Htn1.png"" width
> 900 height 739 supersample 4 transparentBackground true

> color bfactor palette
> 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue

15930 atoms, 2064 residues, atom bfactor range 32.5 to 191  

> select clear

> hide #7 atoms

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Htn1-pLDDT.png""
> width 900 height 739 supersample 4 transparentBackground true

> select clear

> hide #7 models

> open
> /Users/u6290062/Downloads/ghwak7A_70d62/ghwak7A_70d62_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb

Chain information for
ghwak7A_70d62_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb #8  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> open
> /Users/u6290062/Downloads/SlWAK1_f88fd/SlWAK1_f88fd_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb

Chain information for
SlWAK1_f88fd_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb #9  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> hide #8 models

> hide #9 models

> open
> /Users/u6290062/Downloads/rfo1_1159a_0/rfo1_1159a_0_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb

Chain information for
rfo1_1159a_0_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #10  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> hide #10 models

> open
> /Users/u6290062/Downloads/BrWAK1_96657/BrWAK1_96657_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb

Chain information for
BrWAK1_96657_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb #11  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> hide #11 models

> open
> /Users/u6290062/Downloads/AtWAK1_f4e1e/AtWAK1_f4e1e_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb

Chain information for
AtWAK1_f4e1e_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb #12  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> hide #12 models

> open
> /Users/u6290062/Downloads/OsWAK1_3328c/OsWAK1_3328c_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb

Chain information for
OsWAK1_3328c_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #13  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> hide #13 models

> open
> /Users/u6290062/Downloads/OsDEES1_24a01/OsDEES1_24a01_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb

Chain information for
OsDEES1_24a01_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb #14  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Immunity-
> WAKs.cxs"" includeMaps true

> hide #14 models

> show #2 models

> select add #2/A:79

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

> select add #2/A:80

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

> select subtract #2/A:79

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

> select add #2/A:201

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

> select #2/A:80-81

19 atoms, 18 bonds, 2 residues, 1 model selected  

> select #2/A:80-201

946 atoms, 969 bonds, 122 residues, 1 model selected  

> hide sel cartoons

> select clear

> hide #2 atoms

> select clear

> select #2/A:6-7

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

> select #2/A:6-79

559 atoms, 577 bonds, 74 residues, 1 model selected  

> select #2/A:6-79,202-206

609 atoms, 629 bonds, 79 residues, 1 model selected  

> show sel atoms

> select subtract #2/A:23

595 atoms, 612 bonds, 78 residues, 1 model selected  

> select add #2/A:23

609 atoms, 627 bonds, 79 residues, 1 model selected  

> select subtract #2/A:22

598 atoms, 615 bonds, 78 residues, 1 model selected  

> select subtract #2/A:43

590 atoms, 606 bonds, 77 residues, 1 model selected  

> select subtract #2/A:52

582 atoms, 597 bonds, 76 residues, 1 model selected  

> select add #2/A:52

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

> select subtract #2/A:53

582 atoms, 596 bonds, 76 residues, 1 model selected  

> select add #2/A:53

590 atoms, 603 bonds, 77 residues, 1 model selected  

> select subtract #2/A:75

582 atoms, 594 bonds, 76 residues, 1 model selected  

> select subtract #2/A:206@CB

581 atoms, 592 bonds, 76 residues, 1 model selected  

> select add #2/A:206@CB

582 atoms, 592 bonds, 76 residues, 1 model selected  

> select subtract #2/A:18

574 atoms, 584 bonds, 75 residues, 1 model selected  

> select add #2/A:18

582 atoms, 591 bonds, 76 residues, 1 model selected  

> select clear

> select add #2/A:22

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

> select add #2/A:206

25 atoms, 26 bonds, 2 residues, 1 model selected  

> select add #2/A:42

34 atoms, 34 bonds, 3 residues, 1 model selected  

> select add #2/A:41

45 atoms, 45 bonds, 4 residues, 1 model selected  

> select add #2/A:43

53 atoms, 52 bonds, 5 residues, 1 model selected  

> select subtract #2/A:42@CB

52 atoms, 50 bonds, 5 residues, 1 model selected  

> select subtract #2/A:42@OE1

51 atoms, 48 bonds, 5 residues, 1 model selected  

> select subtract #2/A:42@OE2

50 atoms, 47 bonds, 5 residues, 1 model selected  

> select add #2/A:52

58 atoms, 54 bonds, 6 residues, 1 model selected  

> select subtract #2/A:52

50 atoms, 47 bonds, 5 residues, 1 model selected  

> select add #2/A:53

58 atoms, 54 bonds, 6 residues, 1 model selected  

> select add #2/A:65

66 atoms, 61 bonds, 7 residues, 1 model selected  

> select add #2/A:75

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

> select add #2/A:68

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

> select add #2/A:18

90 atoms, 82 bonds, 10 residues, 1 model selected  

> select add #2/A:51

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

> select ~sel & ##selected

1525 atoms, 1580 bonds, 196 residues, 1 model selected  

> hide sel atoms

> select clear

> color #2 byhetero

> select clear

> show #2 cartoons

> select clear

> show #2 atoms

> hide #2 atoms

> color #2 #ebebebff

> select clear

> show #2 surfaces

> hide #!2 surfaces

> select clear

> show #10 models

> hide #10 models

> show #11 models

> hide #11 models

> show #8 models

> hide #8 models

> show #9 models

> hide #9 models

> show #10 models

> hide #10 models

> show #13 models

> show #14 models

> hide #14 models

> select clear

> ui tool show Matchmaker

> matchmaker #13 to #2

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 stb6.pdb, chain A (#2) with
OsWAK1_3328c_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain A
(#13), sequence alignment score = 203.4  
RMSD between 88 pruned atom pairs is 1.029 angstroms; (across all 174 pairs:
5.037)  
  

> select clear

> select add #13/A:41

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

> select add #13/A:42

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

> select add #13/A:43

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

> setattr #13:41-43 res ss_type 2

Assigning ss_type attribute to 3 items  

> select clear

> hide #!2 models

> select clear

> select add #13/A:77

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

> select add #13/A:76

20 atoms, 18 bonds, 2 residues, 1 model selected  

> select #13/A:77

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

> select #13/A:77

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

> select #13/A:76

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

> select add #13/A:96

17 atoms, 15 bonds, 2 residues, 1 model selected  

> setattr #13:76-96 res ss_type 0

Assigning ss_type attribute to 21 items  

> select clear

> select add #13/A:175

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

> select add #13/A:174

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

> select add #13/A:173

20 atoms, 18 bonds, 3 residues, 1 model selected  

> setattr #13:173-175 res ss_type 0

Assigning ss_type attribute to 3 items  

> select clear

> select ::name=""GLN""

954 atoms, 853 bonds, 106 residues, 14 models selected  

> select ::name=""CYS""

1644 atoms, 1440 bonds, 274 residues, 14 models selected  

> show sel & #13 atoms

> select clear

> select add #13/A:86@SG

1 atom, 1 residue, 1 model selected  

> select add #13/A:135@SG

2 atoms, 2 residues, 1 model selected  

> select add #13/A:160@SG

3 atoms, 3 residues, 1 model selected  

> select add #13/A:116@SG

4 atoms, 4 residues, 1 model selected  

> bond sel

Created 2 bonds  

> select clear

> select add #13/A:47@SG

1 atom, 1 residue, 1 model selected  

> select add #13/A:7@SG

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select add #13/A:2@SG

3 atoms, 3 residues, 1 model selected  

> select add #13/A:38@SG

4 atoms, 4 residues, 1 model selected  

> bond sel

Created 1 bond  

> select clear

> select add #13/A:236@SG

1 atom, 1 residue, 1 model selected  

> select add #13/A:226@SG

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select add #13/A:205@SG

3 atoms, 3 residues, 1 model selected  

> select add #13/A:224@SG

4 atoms, 4 residues, 1 model selected  

> bond sel

Created 1 bond  

> select add #13/A:202@SG

5 atoms, 5 residues, 1 model selected  

> select subtract #13/A:202@SG

4 atoms, 4 residues, 1 model selected  

> select add #13/A:202@SG

5 atoms, 5 residues, 1 model selected  

> select add #13/A:212@SG

6 atoms, 6 residues, 1 model selected  

> bond sel

Created 1 bond  

> select clear

> select add #13/A:194

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select add #13/A:168

22 atoms, 22 bonds, 2 residues, 1 model selected  
Alignment identifier is 13/A  

> select #13/A:168

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

> select #13/A:168-194

218 atoms, 227 bonds, 27 residues, 1 model selected  

> color sel forest green target ac

> select clear

> select add #13/A:75

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

> select add #13/A:76

19 atoms, 18 bonds, 2 residues, 1 model selected  

> select subtract #13/A:75

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

> select add #13/A:107

17 atoms, 15 bonds, 2 residues, 1 model selected  

> select #13/A:76

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

> select #13/A:76-107

230 atoms, 232 bonds, 32 residues, 1 model selected  

> color sel light gray target ac

> select clear

> select add #13/A:108

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

> select add #13/A:166

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select subtract #13/A:166

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

> select add #13/A:167

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

> select #13/A:108

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

> select #13/A:108-167

453 atoms, 466 bonds, 60 residues, 1 model selected  

> color sel dark khaki target ac

> select clear

> select add #13/A:195

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

> select #13/A:195

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

> select #13/A:195-243

348 atoms, 354 bonds, 49 residues, 1 model selected  

> color sel light steel blue target ac

> select clear

> select add #13/A:75

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

> select #13/A:74-75

15 atoms, 15 bonds, 2 residues, 1 model selected  

> select #13/A:1-75

555 atoms, 573 bonds, 75 residues, 1 model selected  

> color sel dark sea green target ac

> select clear

> select ::name=""CYS""

1644 atoms, 1447 bonds, 274 residues, 14 models selected  

> color (#13 & sel) byhetero

> select clear

> select #13/A:195

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

> color sel forest green target ac

> select clear

> select ::name=""ASN""

2336 atoms, 2057 bonds, 292 residues, 14 models selected  

> select clear

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/OsWAK1.png""
> width 900 height 739 supersample 4 transparentBackground true

> select clear

> color bfactor palette
> 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue

32381 atoms, 4250 residues, 1 surfaces, atom bfactor range 28.5 to 191  

> hide #13 atoms

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity
> WAKs/OsWAK1-pLDDT.png"" width 900 height 739 supersample 4
> transparentBackground true

> hide #13 models

> show #14 models

> close #14

> select clear

> show #11 models

> color #11 darkgrey

> select clear

> show #!2 models

> color #2 #00fdffff

> select clear

> ui tool show Matchmaker

> matchmaker #!2 to #11

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
BrWAK1_96657_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb, chain A
(#11) with stb6.pdb, chain A (#2), sequence alignment score = 102.1  
RMSD between 31 pruned atom pairs is 0.917 angstroms; (across all 168 pairs:
14.481)  
  

> select clear

> select add #11/A:43

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

> select add #11/A:45

19 atoms, 18 bonds, 2 residues, 1 model selected  

> setattr #11:43-45 res ss_type 0

Assigning ss_type attribute to 3 items  

> setattr #11:43-45 res ss_type 2

Assigning ss_type attribute to 3 items  

> select clear

> select add #11/A:33

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

> select add #11/A:31

18 atoms, 18 bonds, 2 residues, 1 model selected  

> setattr #11:31-33 res ss_type 0

Assigning ss_type attribute to 3 items  

> select clear

> select #11/A:33

11 atoms, 11 bonds, 1 residue, 1 model selected  
Alignment identifier is 11/A  

> select #11/A:34

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

> select #11/A:34-35

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #11/A:33-34

19 atoms, 19 bonds, 2 residues, 1 model selected  

> select #11/A:33-35

27 atoms, 27 bonds, 3 residues, 1 model selected  

> select #2/A:194

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

> select #2/A:194-195

21 atoms, 21 bonds, 2 residues, 1 model selected  

> select clear

> select #11/A:33

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

> select #11/A:33-35

27 atoms, 27 bonds, 3 residues, 1 model selected  

> select add #11/A:38

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

> select #11/A:33-34

19 atoms, 19 bonds, 2 residues, 1 model selected  

> select #11/A:33-40

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

> setattr #11:33-40 res ss_type 2

Assigning ss_type attribute to 8 items  

> select clear

> setattr #11:33-40 res ss_type 0

Assigning ss_type attribute to 8 items  

> select add #11/A:36

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

> select add #11/A:38

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

> setattr #11:36-38 res ss_type 2

Assigning ss_type attribute to 3 items  

> select clear

> select #11/A:35

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

> select add #11/A:32

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

> setattr #11:32-35 res ss_type 2

Assigning ss_type attribute to 4 items  

> setattr #11:32-35 res ss_type 0

Assigning ss_type attribute to 4 items  

> setattr #11:36-38 res ss_type 2

Assigning ss_type attribute to 3 items  

> select clear

> select add #11/A:32

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

> select add #11/A:34

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

> select #11/A:33

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

> select #11/A:33-35

27 atoms, 27 bonds, 3 residues, 1 model selected  

> setattr #11:32-34 res ss_type 2

Assigning ss_type attribute to 3 items  

> select clear

> setattr #11:31-34 res ss_type 2

Assigning ss_type attribute to 4 items  

> select clear

> select add #11/A:19

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

> select add #11/A:21

18 atoms, 17 bonds, 2 residues, 1 model selected  

> setattr #11:19-21 res ss_type 2

Assigning ss_type attribute to 3 items  

> select clear

> hide #!2 models

> select clear

> select add #11/A:305

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

> select #11/A:305

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

> select #11/A:305-311

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

> hide sel cartoons

> select clear

> select ::name=""CYS""

1512 atoms, 1336 bonds, 252 residues, 13 models selected  

> show sel & #11 atoms

> color (#11 & sel) byelement

> select clear

> select add #11/A:10@SG

1 atom, 1 residue, 1 model selected  

> select add #11/A:37@SG

2 atoms, 2 residues, 1 model selected  

> select add #11/A:6@SG

3 atoms, 3 residues, 1 model selected  

> select add #11/A:25@SG

4 atoms, 4 residues, 1 model selected  

> select add #11/A:221@SG

5 atoms, 5 residues, 1 model selected  

> select add #11/A:239@SG

6 atoms, 6 residues, 1 model selected  

> select add #11/A:257@SG

7 atoms, 7 residues, 1 model selected  

> select add #11/A:241@SG

8 atoms, 8 residues, 1 model selected  

> select add #11/A:212@SG

9 atoms, 9 residues, 1 model selected  

> select add #11/A:228@SG

10 atoms, 10 residues, 1 model selected  

> select add #11/A:278@SG

11 atoms, 11 residues, 1 model selected  

> select add #11/A:263@SG

12 atoms, 12 residues, 1 model selected  

> select clear

> select S

288 atoms, 68 bonds, 288 residues, 13 models selected  

> bond sel

Created 55 bonds  

> select clear

> select add #11/A:206

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

> select add #11/A:179

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

> color sel forest green target ac

> select #11/A:179

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

> select #11/A:179-206

233 atoms, 239 bonds, 28 residues, 1 model selected  

> color sel forest green target ac

> select clear

> select add #11/A:94

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

> select add #11/A:93

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

> select subtract #11/A:94

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

> select add #11/A:64

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

> select subtract #11/A:64

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

> select add #11/A:65

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

> select #11/A:93

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

> select #11/A:65-93

220 atoms, 223 bonds, 29 residues, 1 model selected  

> color sel light gray target ac

> select clear

> select add #11/A:64

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

> select #11/A:64

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

> select #11/A:1-64

513 atoms, 527 bonds, 64 residues, 1 model selected  

> color sel dark sea green target ac

> select clear

> select add #11/A:94

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

> select add #11/A:178

17 atoms, 15 bonds, 2 residues, 1 model selected  

> select #11/A:94

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

> select #11/A:94-178

624 atoms, 641 bonds, 85 residues, 1 model selected  

> color sel dark khaki target ac

> select clear

> select add #11/A:207

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

> select #11/A:207

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

> select #11/A:207-311

802 atoms, 819 bonds, 105 residues, 1 model selected  

> color sel light steel blue target ac

> select clear

> select ::name=""CYS""

1512 atoms, 1391 bonds, 252 residues, 13 models selected  

> color (#11 & sel) byhetero

> select clear

> select #11/A:3

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

> select #11/A:1-3

27 atoms, 27 bonds, 3 residues, 1 model selected  

> hide sel cartoons

> select clear

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/BrWAK1.png""
> width 900 height 739 supersample 4 transparentBackground true

> select clear

> color bfactor palette
> 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue

29737 atoms, 3887 residues, 1 surfaces, atom bfactor range 28.5 to 191  

> select clear

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity
> WAKs/BrWAK1-pLDDT.png"" width 900 height 739 supersample 4
> transparentBackground true

> select clear

> hide #11 models

> show #12 models

> color #12 #008f00ff

> select clear

> show #!2 models

> color #2 #ebebebff

> select clear

> ui tool show ""Render/Select by Attribute""

> ui tool show Matchmaker

> matchmaker #12 to #2

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 stb6.pdb, chain A (#2) with
AtWAK1_f4e1e_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb, chain A
(#12), sequence alignment score = 130.5  
RMSD between 34 pruned atom pairs is 0.976 angstroms; (across all 170 pairs:
17.148)  
  

> select add #12/A:34

6 atoms, 5 bonds, 1 residue, 1 model selected  
Alignment identifier is 12/A  

> select clear

> select add #12/A:34

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

> select add #12/A:35

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

> setattr #12:34-35 res ss_type 0

Assigning ss_type attribute to 2 items  

> select #12/A:35

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

> select #12/A:35-37

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

> setattr #12:35-37 res ss_type 2

Assigning ss_type attribute to 3 items  

> select clear

> select add #12/A:21

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

> select add #12/A:23

19 atoms, 18 bonds, 2 residues, 1 model selected  

> setattr #12:21-23 res ss_type 2

Assigning ss_type attribute to 3 items  

> select clear

> hide #!2 models

> select ::name=""CYS""

1512 atoms, 1391 bonds, 252 residues, 13 models selected  

> show sel & #12 atoms

> color (#12 & sel) byhetero

> select clear

> select add #12/A:7

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

> select #12/A:6

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

> select #12/A:5-6

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

> select #12/A:1

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

> select #12/A:1-5

39 atoms, 40 bonds, 5 residues, 1 model selected  

> hide sel cartoons

> select clear

> select add #12/A:306

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

> select #12/A:306

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

> select #12/A:306-312

62 atoms, 64 bonds, 7 residues, 1 model selected  

> hide sel cartoons

> select clear

> select add #12/A:67

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

> select add #12/A:95

19 atoms, 17 bonds, 2 residues, 1 model selected  

> select #12/A:67

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

> select #12/A:67-95

225 atoms, 226 bonds, 29 residues, 1 model selected  

> color sel light gray target ac

> select clear

> select add #12/A:96

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

> select add #12/A:180

17 atoms, 15 bonds, 2 residues, 1 model selected  

> select add #12/A:181

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

> select #12/A:96

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

> select #12/A:96-181

645 atoms, 661 bonds, 86 residues, 1 model selected  

> color sel dark khaki target ac

> select clear

> select add #12/A:66

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

> select add #12/A:6

17 atoms, 15 bonds, 2 residues, 1 model selected  

> select #12/A:6

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

> select #12/A:6-66

475 atoms, 487 bonds, 61 residues, 1 model selected  

> color sel dark sea green target ac

> select clear

> select #12/A:6

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

> select #12/A:6

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

> hide sel cartoons

> select clear

> select add #12/A:207

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select add #12/A:208

20 atoms, 20 bonds, 2 residues, 1 model selected  

> select subtract #12/A:207

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

> select #12/A:208

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

> select #12/A:208-312

790 atoms, 809 bonds, 105 residues, 1 model selected  

> color sel light steel blue target ac

> select clear

> select ::name=""CYS""

1512 atoms, 1391 bonds, 252 residues, 13 models selected  

> color (#12 & sel) byhetero

> select clear

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/AtWAK1.png""
> width 900 height 739 supersample 4 transparentBackground true

> color bfactor palette
> 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue

29737 atoms, 3887 residues, 1 surfaces, atom bfactor range 28.5 to 191  

> select clear

> hide #12 atoms

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity
> WAKs/AtWAK1-pLDDT.png"" width 900 height 739 supersample 4
> transparentBackground true

> select clear

> hide #12 models

> show #10 models

> select clear

> color #10 darkgrey

> show #!2 models

> color #2 #73fa79ff

> select clear

> ui tool show Matchmaker

> matchmaker #!2 to #10

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
rfo1_1159a_0_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain A
(#10) with stb6.pdb, chain A (#2), sequence alignment score = 73.3  
RMSD between 37 pruned atom pairs is 0.894 angstroms; (across all 154 pairs:
13.896)  
  

> select clear

> select #2/A:25

7 atoms, 6 bonds, 1 residue, 1 model selected  
Destroying pre-existing alignment with identifier 2/A  
Alignment identifier is 2/A  
Destroying pre-existing alignment with identifier 2/A  
Alignment identifier is 2/A  
Destroying pre-existing alignment with identifier 2/A  
Alignment identifier is 2/A  

> select clear

> select #10/A:26

4 atoms, 3 bonds, 1 residue, 1 model selected  
Alignment identifier is 10/A  

> select clear

> select add #10/A:36

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

> select add #10/A:34

20 atoms, 19 bonds, 2 residues, 1 model selected  

> setattr #10:36-39 res ss_type 0

Assigning ss_type attribute to 4 items  

> select #10/A:63

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

> select add #10/A:34

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

> select add #10/A:35

30 atoms, 29 bonds, 3 residues, 1 model selected  

> setattr #10:34-36 res ss_type 0

Assigning ss_type attribute to 3 items  

> select add #10/A:38

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

> select subtract #10/A:35

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

> select add #10/A:35

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

> select subtract #10/A:34

29 atoms, 28 bonds, 3 residues, 1 model selected  

> setattr #10:34-35 res ss_type 2

Assigning ss_type attribute to 2 items  

> setattr #10:34-36 res ss_type 2

Assigning ss_type attribute to 3 items  

> setattr #10:34-37 res ss_type 2

Assigning ss_type attribute to 4 items  

> setattr #10:34-38 res ss_type 2

Assigning ss_type attribute to 5 items  

> select add #10/A:34

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

> select clear

> select add #10/A:34

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

> select add #10/A:35

22 atoms, 22 bonds, 2 residues, 1 model selected  

> setattr #10:34-35 res ss_type 0

Assigning ss_type attribute to 2 items  

> select clear

> select add #10/A:23

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

> select add #10/A:25

19 atoms, 18 bonds, 2 residues, 1 model selected  

> select clear

> select add #10/A:23

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

> select add #10/A:25

19 atoms, 18 bonds, 2 residues, 1 model selected  

> setattr #10:23-25 res ss_type 2

Assigning ss_type attribute to 3 items  

> select clear

> select add #10/A:30

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

> select add #10/A:29

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

> select add #10/A:28

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

> setattr #10:28-29 res ss_type 0

Assigning ss_type attribute to 2 items  

> select clear

> hide #!2 models

> select clear

> select ::name=""CYS""

1512 atoms, 1391 bonds, 252 residues, 13 models selected  

> show sel & #10 atoms

> color (#10 & sel) byhetero

> select clear

> select S

288 atoms, 123 bonds, 288 residues, 13 models selected  

> bond sel

Created 0 bonds  

> select clear

> select add #10/A:275

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

> select #10/A:275

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

> select #10/A:275-287

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

> hide sel cartoons

> select clear

> select add #10/A:9

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

> select #10/A:8

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

> select #10/A:1-8

54 atoms, 55 bonds, 8 residues, 1 model selected  

> hide sel cartoons

> select clear

> select add #10/A:138

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

> select add #10/A:146

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

> setattr #10/A:138-146 res ss_type 1

Assigning ss_type attribute to 9 items  

> setattr #10/A:138-146 res ss_type 0

Assigning ss_type attribute to 9 items  

> select clear

> select add #10/A:82

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

> select add #10/A:112

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

> color sel light gray target ac

> select #10/A:82

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

> select #10/A:82-112

227 atoms, 232 bonds, 31 residues, 1 model selected  

> color sel light gray target ac

> select clear

> select add #10/A:81

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

> select add #10/A:9

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

> select #10/A:9

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

> select #10/A:9-81

570 atoms, 585 bonds, 73 residues, 1 model selected  

> color sel dark sea green target ac

> select clear

> select add #10/A:182

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

> select add #10/A:155

20 atoms, 19 bonds, 2 residues, 1 model selected  

> select #10/A:155

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

> select #10/A:155-182

232 atoms, 240 bonds, 28 residues, 1 model selected  

> color sel forest green target ac

> select clear

> select add #10/A:113

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

> select add #10/A:154

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

> select #10/A:113

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

> select #10/A:113-154

298 atoms, 300 bonds, 42 residues, 1 model selected  

> color sel dark khaki target ac

> select clear

> select add #10/A:183

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

> select #10/A:183

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

> select #10/A:183-287

778 atoms, 801 bonds, 105 residues, 1 model selected  

> color sel light steel blue target ac

> select clear

> select ::name=""CYS""

1512 atoms, 1391 bonds, 252 residues, 13 models selected  

> color (#10 & sel) byhetero

> select clear

> select add #10/A:131

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

> select add #10/A:130

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

> select add #10/A:134

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

> setattr #10/A:130-134 res ss_type 2

Assigning ss_type attribute to 5 items  

> select clear

> select add #10/A:123

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

> select add #10/A:118

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

> setattr #10/A:118-123 res ss_type 2

Assigning ss_type attribute to 6 items  

> select clear

> setattr #10/A:118-123 res ss_type 0

Assigning ss_type attribute to 6 items  

> setattr #10/A:119-123 res ss_type 2

Assigning ss_type attribute to 5 items  

> select clear

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Rfo1.png"" width
> 900 height 739 supersample 4 transparentBackground true

> select clear

> color bfactor palette
> 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue

29737 atoms, 3887 residues, 1 surfaces, atom bfactor range 28.5 to 191  

> select clear

> hide #10 atoms

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Rfo1-pLDDT.png""
> width 900 height 739 supersample 4 transparentBackground true

> select clear

> hide #10 models

> show #8 models

> select clear

> color #8 white

> select clear

> show #!2 models

> color #2 #797979ff

> ui tool show Matchmaker

> matchmaker #!2 to #8

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
ghwak7A_70d62_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb, chain A
(#8) with stb6.pdb, chain A (#2), sequence alignment score = 67.2  
RMSD between 48 pruned atom pairs is 0.996 angstroms; (across all 172 pairs:
13.707)  
  

> select clear

> select add #8/A:37

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

> select add #8/A:33

17 atoms, 15 bonds, 2 residues, 1 model selected  

> setattr #8:33-37 res ss_type 0

Assigning ss_type attribute to 5 items  

> select clear

> select #8/A:35

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

> select add #8/A:37

19 atoms, 18 bonds, 2 residues, 1 model selected  

> setattr #8:35-37 res ss_type 2

Assigning ss_type attribute to 3 items  

> select clear

> select add #8/A:20

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

> select clear

> select add #8/A:23

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

> select add #8/A:25

18 atoms, 17 bonds, 2 residues, 1 model selected  

> setattr #8:25-23 res ss_type 2

Assigning ss_type attribute to 0 items  

> setattr #8:23-25 res ss_type 2

Assigning ss_type attribute to 3 items  

> select clear

> hide #!2 models

> select ::name=""CYS""

1512 atoms, 1391 bonds, 252 residues, 13 models selected  

> show sel & #8 atoms

> color (#8 & sel) byhetero

> select clear

> select add #8/A:151@SG

1 atom, 1 residue, 1 model selected  

> select clear

> select #8/A:130@SG

1 atom, 1 residue, 1 model selected  

> select add #8/A:151@SG

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 0 bonds  

> select clear

> select add #8/A:215

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

> select add #8/A:189

20 atoms, 19 bonds, 2 residues, 1 model selected  
Alignment identifier is 8/A  

> select #8/A:189

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

> select #8/A:189-215

230 atoms, 236 bonds, 27 residues, 1 model selected  

> color sel forest green target ac

> select clear

> select add #8/A:188

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

> select add #8/A:104

17 atoms, 15 bonds, 2 residues, 1 model selected  

> select #8/A:104

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

> select #8/A:104-188

645 atoms, 660 bonds, 85 residues, 1 model selected  

> color sel dark khaki target ac

> select clear

> select add #8/A:72

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

> select #8/A:72

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

> select #8/A:1-72

557 atoms, 572 bonds, 72 residues, 1 model selected  

> color sel dark sea green target ac

> select clear

> select add #8/A:9

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

> select #8/A:8

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

> select #8/A:1-8

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

> hide sel cartoons

> select clear

> select add #8/A:216

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

> select #8/A:216

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

> select #8/A:216-318

753 atoms, 769 bonds, 103 residues, 1 model selected  

> color sel light steel blue target ac

> select clear

> select add #8/A:311

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

> select #8/A:312

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

> select #8/A:312-318

42 atoms, 41 bonds, 7 residues, 1 model selected  

> select #8/A:311

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

> select #8/A:311-318

49 atoms, 48 bonds, 8 residues, 1 model selected  

> hide sel cartoons

> select clear

> select ::name=""CYS""

1512 atoms, 1391 bonds, 252 residues, 13 models selected  

> color (#8 & sel) byhetero

> select clear

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/GhWAK7A.png""
> width 900 height 739 supersample 4 transparentBackground true

> select clear

> color bfactor palette
> 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue

29737 atoms, 3887 residues, 1 surfaces, atom bfactor range 28.5 to 191  

> select clear

> hide #8 atoms

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity
> WAKs/GhWAK7A-pLDDT.png"" width 900 height 739 supersample 4
> transparentBackground true

> select clear

> hide #8 models

> show #9 models

> select clear

> color #9 white

> show #!2 models

> color #2 #5e5e5eff

> hide #!2 models

> select add #9/A:65

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

> select add #9/A:66

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

> select add #9/A:67

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

> setattr #9:65-67 res ss_type 0

Assigning ss_type attribute to 3 items  

> select clear

> select add #9/A:67

11 atoms, 11 bonds, 1 residue, 1 model selected  
Alignment identifier is 9/A  

> select #9/A:67

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

> select #9/A:67-69

28 atoms, 28 bonds, 3 residues, 1 model selected  

> setattr #9:67-69 res ss_type 2

Assigning ss_type attribute to 3 items  

> select clear

> setattr #9:66-69 res ss_type 2

Assigning ss_type attribute to 4 items  

> setattr #9:66-70 res ss_type 2

Assigning ss_type attribute to 5 items  

> setattr #9:66-70 res ss_type 2

Assigning ss_type attribute to 5 items  

> select add #9/A:65

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

> select add #9/A:66

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

> select add #9/A:67

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

> setattr #9:65-67 res ss_type 0

Assigning ss_type attribute to 3 items  

> select clear

> select add #9/A:55

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

> select add #9/A:57

19 atoms, 18 bonds, 2 residues, 1 model selected  

> setattr #9:55-57 res ss_type 2

Assigning ss_type attribute to 3 items  

> select clear

> select ::name=""CYS""

1512 atoms, 1391 bonds, 252 residues, 13 models selected  

> show sel & #9 atoms

> color (#9 & sel) byhetero

> select clear

> select add #9/A:338

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

> select #9/A:338

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

> select #9/A:338-352

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

> hide sel cartoons

> select clear

> select add #9/A:42

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

> select clear

> select #9/A:41

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

> select #9/A:41

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

> select #9/A:1-41

282 atoms, 290 bonds, 41 residues, 1 model selected  

> hide sel cartoons

> select clear

> select add #9/A:242

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

> select add #9/A:211

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

> select #9/A:211

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

> select #9/A:211-242

260 atoms, 265 bonds, 32 residues, 1 model selected  

> color sel forest green target ac

> select clear

> select add #9/A:210

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

> select add #9/A:130

17 atoms, 15 bonds, 2 residues, 1 model selected  

> select #9/A:130

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

> select #9/A:130-210

604 atoms, 620 bonds, 81 residues, 1 model selected  

> color sel dark khaki target ac

> select clear

> select add #9/A:96

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

> select subtract #9/A:96

Nothing selected  

> select add #9/A:95

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

> select #9/A:95

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

> select #9/A:1-95

688 atoms, 708 bonds, 95 residues, 1 model selected  

> color sel dark sea green target ac

> select clear

> select add #9/A:243

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

> select #9/A:243-244

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

> select #9/A:243-352

811 atoms, 832 bonds, 110 residues, 1 model selected  

> color sel light steel blue target ac

> select clear

> select ::name=""CYS""

1512 atoms, 1391 bonds, 252 residues, 13 models selected  

> color (#9 & sel) byhetero

> select clear

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/SlWAK1.png""
> width 900 height 739 supersample 4 transparentBackground true

> select clear

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/SlWAK1.png""
> width 900 height 739 supersample 4 transparentBackground true

> select clear

> color bfactor palette
> 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue

29737 atoms, 3887 residues, 1 surfaces, atom bfactor range 28.5 to 191  

> select clear

> hide #9 atoms

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity
> WAKs/SlWAK1-pLDDT.png"" width 900 height 739 supersample 4
> transparentBackground true

> select clear

> hide #9 models

> show #7 models

> select clear

> select add #7/A:108

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

> select clear

> select #7/A:109

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

> select add #7/A:62

18 atoms, 16 bonds, 2 residues, 1 model selected  
Alignment identifier is 7/A  

> select #7/A:63

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

> select #7/A:63-64

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select clear

> setattr #9/A:63-64 res ss_type 0

Assigning ss_type attribute to 2 items  

> select clear

> setattr #9/A:63-64 res ss_type 0

Assigning ss_type attribute to 2 items  

> setattr #7/A:63-64 res ss_type 0

Assigning ss_type attribute to 2 items  

> select clear

> select ::name=""CYS""

1512 atoms, 1391 bonds, 252 residues, 13 models selected  

> show sel & #7 atoms

> select clear

> select #7/A:32

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

> select #7/A:32-39

63 atoms, 65 bonds, 8 residues, 1 model selected  

> select #7/A:148

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

> select #7/A:32-148

916 atoms, 945 bonds, 117 residues, 1 model selected  

> select clear

> select add #7/A:108

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

> select add #7/A:139

19 atoms, 18 bonds, 2 residues, 1 model selected  

> select subtract #7/A:139

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

> select add #7/A:138

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

> select subtract #7/A:108

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

> select add #7/A:109

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

> select #7/A:109

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

> select #7/A:109-138

228 atoms, 234 bonds, 30 residues, 1 model selected  

> color sel light gray target ac

> select clear

> select add #7/A:108

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

> select #7/A:108

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

> select #7/A:1-108

828 atoms, 858 bonds, 108 residues, 1 model selected  

> color sel dark sea green target ac

> select clear

> select add #7/A:239

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

> select #7/A:238

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select add #7/A:209

25 atoms, 25 bonds, 2 residues, 1 model selected  

> select #7/A:209

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

> select #7/A:209-239

253 atoms, 257 bonds, 31 residues, 1 model selected  

> color sel forest green target ac

> select clear

> select add #7/A:139

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

> select add #7/A:207

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select subtract #7/A:207

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

> select add #7/A:211

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select add #7/A:208

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

> select subtract #7/A:211

22 atoms, 21 bonds, 2 residues, 1 model selected  

> select #7/A:139-140

19 atoms, 19 bonds, 2 residues, 1 model selected  

> select #7/A:139-208

558 atoms, 577 bonds, 70 residues, 1 model selected  

> color sel dark khaki target ac

> select clear

> select add #7/A:240

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

> select #7/A:240

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

> select #7/A:240-291

383 atoms, 392 bonds, 52 residues, 1 model selected  

> color sel light steel blue target ac

> select clear

> select ::name=""CYS""

1512 atoms, 1391 bonds, 252 residues, 13 models selected  

> color (#7 & sel) byhetero

> select clear

> select add #7/A:48

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

> select add #7/A:60

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

> select #7/A:48

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

> select #7/A:48-60

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

> color sel pale green target ac

> color sel medium aquamarine target ac

> color sel pale green target ac

> color sel lawn green target ac

> color sel medium sea green target ac

> color sel green yellow target ac

> color sel pale green target ac

> select clear

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Htn1.png"" width
> 900 height 739 supersample 4 transparentBackground true

> color bfactor palette
> 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue

29737 atoms, 3887 residues, 1 surfaces, atom bfactor range 28.5 to 191  

> select clear

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Htn1-pLDDT.png""
> width 900 height 739 supersample 4 transparentBackground true

> select clear

> select add #7/A:66

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

> select add #7/A:85

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

> select #7/A:67

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

> select #7/A:67-85

147 atoms, 150 bonds, 19 residues, 1 model selected  

> color sel medium spring green target ac

> color sel chartreuse target ac

> color sel pale green target ac

> color sel olive drab target ac

> select clear

> select add #7/A:66

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

> select #7/A:66

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

> select #7/A:1-66

504 atoms, 526 bonds, 66 residues, 1 model selected  

> color sel dark sea green target ac

> select clear

> select add #7/A:86

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

> select add #7/A:108

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

> select #7/A:86

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

> select #7/A:86-108

177 atoms, 179 bonds, 23 residues, 1 model selected  

> color sel dark sea green target ac

> select clear

> select add #7/A:66

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

> color sel olive drab target ac

> select clear

> select #7/A:66

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

> select add #7/A:85

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

> select #7/A:85

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

> select #7/A:66-85

154 atoms, 157 bonds, 20 residues, 1 model selected  

> color sel dark sea green target ac

> select clear

> select add #7/A:109

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

> select add #7/A:138

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

> select #7/A:109-110

19 atoms, 18 bonds, 2 residues, 1 model selected  

> select #7/A:109-138

228 atoms, 234 bonds, 30 residues, 1 model selected  

> color sel light gray target ac

> select clear

> select add #7/A:208

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

> select subtract #7/A:208

Nothing selected  

> select add #7/A:211

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

> select add #7/A:210

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

> select clear

> select add #7/A:208

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

> select add #7/A:209

22 atoms, 20 bonds, 2 residues, 1 model selected  

> select subtract #7/A:208

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

> select add #7/A:237

20 atoms, 18 bonds, 2 residues, 1 model selected  

> select #7/A:209

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

> select #7/A:209-238

245 atoms, 249 bonds, 30 residues, 1 model selected  

> color sel forest green target ac

> select clear

> select add #7/A:239

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

> select #7/A:239-240

19 atoms, 18 bonds, 2 residues, 1 model selected  

> select #7/A:239-291

391 atoms, 400 bonds, 53 residues, 1 model selected  

> color sel light steel blue target ac

> select clear

> select add #7/A:208

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

> select add #7/A:139

22 atoms, 21 bonds, 2 residues, 1 model selected  

> select #7/A:139

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

> select #7/A:139-208

558 atoms, 577 bonds, 70 residues, 1 model selected  

> color sel dark khaki target ac

> select clear

> select ::name=""CYS""

1512 atoms, 1391 bonds, 252 residues, 13 models selected  

> color (#7 & sel) byhetero

> select clear

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Htn1.png"" width
> 900 height 739 supersample 4 transparentBackground true

> color bfactor palette
> 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue

29737 atoms, 3887 residues, 1 surfaces, atom bfactor range 28.5 to 191  

> select clear

> hide #7 atoms

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Htn1-pLDDT.png""
> width 900 height 739 supersample 4 transparentBackground true

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Immunity-
> WAKs.cxs"" includeMaps true

> select clear

> hide #7 models

> show #4 models

> select clear

> select ::name=""CYS""

1512 atoms, 1391 bonds, 252 residues, 13 models selected  

> show sel & #4 atoms

> color (#4 & sel) byhetero

> select clear

> show #10 models

> hide #4 models

> select clear

> select ::name=""CYS""

1512 atoms, 1391 bonds, 252 residues, 13 models selected  

> show sel & #10 atoms

> select clear

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Immunity-
> WAKs.cxs"" includeMaps true

> hide #10 models

> open 4b43

Summary of feedback from opening 4b43 fetched from pdb  
---  
notes | Fetching compressed mmCIF 4b43 from http://files.rcsb.org/download/4b43.cif  
Fetching CCD IOD from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/IOD/IOD.cif  
Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif  
  
4b43 title:  
Bacterial translation initiation factor IF2 (1-363), apo form, double mutant
K86L H130A [more info...]  
  
Chain information for 4b43 #14  
---  
Chain | Description | UniProt  
A | TRANSLATION INITIATION FACTOR IF-2 | IF2_THET8 1-363  
  
Non-standard residues in 4b43 #14  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
IOD — iodide ion  
MG — magnesium ion  
  
97 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> open 4b43

4b43 title:  
Bacterial translation initiation factor IF2 (1-363), apo form, double mutant
K86L H130A [more info...]  
  
Chain information for 4b43 #15  
---  
Chain | Description | UniProt  
A | TRANSLATION INITIATION FACTOR IF-2 | IF2_THET8 1-363  
  
Non-standard residues in 4b43 #15  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
IOD — iodide ion  
MG — magnesium ion  
  
97 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide #!15 models

> close #14

> close #15

> show #!2 models

> color #2 #ebebebff

> color #2 #d6d6d6ff

> color #2 silver

> select clear

> mlp #!2

Map values for surface ""stb6.pdb_A SES surface"": minimum -28.96, mean -4.218,
maximum 22  
To also show corresponding color key, enter the above mlp command and add key
true  

> open kdHydrophobicity.defattr

No such file/path: kdHydrophobicity.defattr  

> open /Users/u6290062/Downloads/kdHydrophobicity.defattr.txt

Unrecognized file suffix '.txt'  

> open kdHydrophobicity.defattr

No such file/path: kdHydrophobicity.defattr  

> open /Users/u6290062/Downloads/kdHydrophobicity.defattr

Summary of feedback from opening
/Users/u6290062/Downloads/kdHydrophobicity.defattr  
---  
note | Assigned attribute 'kdHydrophobicity' to 3882 residues using match mode: any  
  

> hide #!2 surfaces

> ui tool show ""Render/Select by Attribute""

> color byattribute r:kdHydrophobicity #1,3-13#!2 target csab palette
> -4.5,#ffcc00:0,white:4.5,#33cccc

29737 atoms, 3887 residues, 1 surfaces, atom kdHydrophobicity range -4.5 to
4.5  

> color byattribute r:kdHydrophobicity #1,3-13#!2 target csab palette
> -4.5,#ffcc00:0,white:4.5,#33cccc

29737 atoms, 3887 residues, 1 surfaces, atom kdHydrophobicity range -4.5 to
4.5  

> show #!2 surfaces

> mlp #!2

Map values for surface ""stb6.pdb_A SES surface"": minimum -28.96, mean -4.218,
maximum 22  
To also show corresponding color key, enter the above mlp command and add key
true  

> ui tool show ""Find Cavities""

pyKVFinder module not installed; fetching from PyPi repository...  

Errors may have occurred when running pip:  

pip standard error:  
\---  
ERROR: pip's dependency resolver does not currently take into account all the
packages that are installed. This behaviour is the source of the following
dependency conflicts.  
nptyping 2.5.0 requires numpy=1.20.0; python_version >= ""3.8"", but you
have numpy 2.2.6 which is incompatible.  
chimerax-bundlebuilder 1.5.1 requires numpy==1.26.4, but you have numpy 2.2.6
which is incompatible.  
\---  

pip standard output:  
\---  
\---  

pyKVFinder module installed from PyPi repository.  

> kvfinder #2

14 cavities found for stb6.pdb #2  
stb6.pdb Cavities  
---  
ID |  | Volume | Area | Points | Maximum  
Depth | Average  
Depth  
2.2.7 |  | 64.58 | 88.55 | 299 | 0 | 0  
2.2.3 |  | 60.05 | 71.51 | 278 | 4.07 | 1.76  
2.2.11 |  | 57.24 | 63.53 | 265 | 3 | 0.88  
2.2.2 |  | 56.16 | 67.78 | 260 | 2.55 | 0.75  
2.2.6 |  | 48.82 | 55.81 | 226 | 2.55 | 0.84  
2.2.1 |  | 42.34 | 53.49 | 196 | 2.4 | 0.75  
2.2.8 |  | 31.32 | 51.28 | 145 | 0 | 0  
2.2.12 |  | 22.46 | 41.55 | 104 | 1.34 | 0.37  
2.2.5 |  | 22.03 | 26.54 | 102 | 1.7 | 0.49  
2.2.10 |  | 17.28 | 26.3 | 80 | 0.85 | 0.19  
2.2.14 |  | 8.42 | 16.15 | 39 | 1.04 | 0.47  
2.2.4 |  | 6.48 | 15.25 | 30 | 1.04 | 0.36  
2.2.9 |  | 5.83 | 11.19 | 27 | 0.6 | 0.18  
2.2.13 |  | 5.18 | 9.36 | 24 | 0.6 | 0.05  
  

Populating font family aliases took 68 ms. Replace uses of missing font family
""Times"" with one that exists to avoid this cost.  

> view #2.2.7 @ zoom 0.75

moved plane near -20.493345654074655 [ 0.73049246 -0.67271407 -0.11762899]  
moved plane far -20.493345654074655 [ 0.73049246 -0.67271407 -0.11762899]  

> surface #2.2.1-14 transparency 50

> ~surface #2.2

> surface #2.2.7

> show #!2/A:82,85,119,121,144,154,177,179,194,198

> view #!2.2.3 @ zoom 0.75

moved plane near -22.564736841553437 [0.80196687 0.54550576 0.2434598 ]  
moved plane far -22.564736841553437 [0.80196687 0.54550576 0.2434598 ]  

> ~surface #2.2

> surface #!2.2.3

> show #!2/A:40,53-56,63,105-107,110

> view #!2.2.11 @ zoom 0.75

moved plane near -25.356174459232662 [0.80196687 0.54550576 0.2434598 ]  
moved plane far -25.356174459232662 [0.80196687 0.54550576 0.2434598 ]  

> ~surface #2.2

> surface #!2.2.11

> show #!2/A:139-144,154,190-191,194

> view #!2.2.2 @ zoom 0.75

moved plane near -24.73322198826226 [0.80196687 0.54550576 0.2434598 ]  
moved plane far -24.73322198826226 [0.80196687 0.54550576 0.2434598 ]  

> ~surface #2.2

> surface #!2.2.2

> show #!2/A:101-103,112,118,160,166,178-180

> view #!2.2.6 @ zoom 0.75

moved plane near -22.928707369992463 [0.03014309 0.96483721 0.26111418]  
moved plane far -22.928707369992463 [0.03014309 0.96483721 0.26111418]  

> ~surface #2.2

> surface #!2.2.6

> show #!2/A:99,121-123,147,152,175-177

> view #!2.2.1 @ zoom 0.75

moved plane near -26.063677987837806 [0.03014309 0.96483721 0.26111418]  
moved plane far -26.063677987837806 [0.03014309 0.96483721 0.26111418]  

> ~surface #2.2

> surface #!2.2.1

> show #!2/A:120,122,165-167,169-171,176,178

> view #!2.2.8 @ zoom 0.75

moved plane near -22.54676136699045 [0.03014309 0.96483721 0.26111418]  
moved plane far -22.54676136699045 [0.03014309 0.96483721 0.26111418]  

> ~surface #2.2

> surface #!2.2.8

> show #!2/A:77-79,179-181,197-198,201-202

> view #!2.2.12 @ zoom 0.75

moved plane near -23.470300999803538 [0.03014309 0.96483721 0.26111418]  
moved plane far -23.470300999803538 [0.03014309 0.96483721 0.26111418]  

> ~surface #2.2

> surface #!2.2.12

> show #!2/A:184-187,189,192-193,196

> view #!2.2.5 @ zoom 0.75

moved plane near -22.107261522120314 [0.03014309 0.96483721 0.26111418]  
moved plane far -22.107261522120314 [0.03014309 0.96483721 0.26111418]  

> ~surface #2.2

> surface #!2.2.5

> show #!2/A:7-9,20-23,34-35

> view #!2.2.10 @ zoom 0.75

moved plane near -20.85830133915867 [-0.8452746 0.52288355 0.11001686]  
moved plane far -20.85830133915867 [-0.8452746 0.52288355 0.11001686]  

> ~surface #2.2

> surface #!2.2.10

> show #!2/A:60-61,81,97-100

> view #!2.2.14 @ zoom 0.75

moved plane near -13.816832238616934 [-0.8452746 0.52288355 0.11001686]  
moved plane far -13.816832238616934 [-0.8452746 0.52288355 0.11001686]  

> ~surface #2.2

> surface #!2.2.14

> show #!2/A:84,89,93,145-146

> view #!2.2.4 @ zoom 0.75

moved plane near -16.26052353022109 [-0.8452746 0.52288355 0.11001686]  
moved plane far -16.26052353022109 [-0.8452746 0.52288355 0.11001686]  

> ~surface #2.2

> surface #!2.2.4

> show #!2/A:124,128,132,171,174

> view #!2.2.9 @ zoom 0.75

moved plane near -17.252922620453052 [-0.8452746 0.52288355 0.11001686]  
moved plane far -17.252922620453052 [-0.8452746 0.52288355 0.11001686]  

> ~surface #2.2

> surface #!2.2.9

> show #!2/A:16-17,67-68

> view #!2.2.13 @ zoom 0.75

moved plane near -9.948138531668237 [-0.8452746 0.52288355 0.11001686]  
moved plane far -9.948138531668237 [-0.8452746 0.52288355 0.11001686]  

> ~surface #2.2

> surface #!2.2.13

> show #!2/A:46,50,80,92-93

> ui tool show ""Side View""

> select clear

> close #2.2

> hide #!2 surfaces

> show #!2 surfaces

> hide #!2 surfaces

> show #!2 surfaces

> select clear

> hide #!2 surfaces

> select clear

> select #2/A:80

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

> select add #2/A:200

14 atoms, 12 bonds, 2 residues, 2 models selected  

> select #2/A:80

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

> select #2/A:80-201

946 atoms, 969 bonds, 122 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> select clear

> mlp #!2

Map values for surface ""stb6.pdb_A SES surface"": minimum -28.96, mean -4.218,
maximum 22  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide #!2 surfaces

> select clear

> ui tool show ""Render/Select by Attribute""

> color byattribute r:kdHydrophobicity #!2 target csab palette
> -4.5,#339999:0,white:4.5,#cc9933

1622 atoms, 206 residues, 1 surfaces, atom kdHydrophobicity range -4.5 to 4.5  

> select clear

> color #2 byhetero

> select clear

> select #2/A:9

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

> select #2/A:9

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

> select #2/A:13

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

> select #2/A:13

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

> show sel atoms

> select #2/A:33

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

> select #2/A:33

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

> show sel atoms

> select #2/A:45

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

> select #2/A:45

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

> show sel atoms

> select clear

> ui tool show Distances

> select #2/A:9@SG

1 atom, 1 residue, 1 model selected  

> select add #2/A:45@CB

2 atoms, 2 residues, 1 model selected  

> distance #2/A:9@SG #2/A:45@CB

Distance between stb6.pdb #2/A CYS 9 SG and CYS 45 CB: 9.665Å  

> select clear

> select #2/A:206

14 atoms, 15 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> select #2/A:33@SG

1 atom, 1 residue, 1 model selected  

> select add #2/A:54@CG

2 atoms, 2 residues, 2 models selected  

> distance #2/A:33@SG #2/A:54@CG

Distance between stb6.pdb #2/A CYS 33 SG and PRO 54 CG: 15.517Å  

> distance style dashes 10

> distance style dashes 11

> distance style dashes 12

> distance style dashes 13

> distance style dashes 14

> distance style dashes 15

> distance style dashes 16

> distance style dashes 15

> distance style dashes 10

> select clear

> show #!2 cartoons

> select clear

> hide #!2 atoms

> select clear

> show #7 models

> show #5 models

> ui tool show Matchmaker

> matchmaker #5 to #2

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 stb6.pdb, chain A (#2) with
snn1_d97b8_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain A
(#5), sequence alignment score = 78.7  
RMSD between 44 pruned atom pairs is 0.933 angstroms; (across all 166 pairs:
14.577)  
  

> ui tool show Matchmaker

> matchmaker #7 to #2

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 stb6.pdb, chain A (#2) with
Htn1_00234_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain A
(#7), sequence alignment score = 103.3  
RMSD between 69 pruned atom pairs is 0.971 angstroms; (across all 182 pairs:
9.215)  
  

> ui mousemode right ""translate selected models""

> select add #5

2645 atoms, 2735 bonds, 346 residues, 1 model selected  

> view matrix models
> #5,0.19339,-0.91678,-0.34945,97.757,0.8353,-0.032979,0.5488,3.8581,-0.51465,-0.39803,0.75941,49.25

> select subtract #5

Nothing selected  

> select add #7

2250 atoms, 2323 bonds, 291 residues, 1 model selected  

> view matrix models
> #7,0.29983,0.71847,-0.62762,50.42,-0.28833,-0.55887,-0.77751,-4.0589,-0.90938,0.41408,0.03959,22.758

> select clear

> select #7/A:71

9 atoms, 8 bonds, 1 residue, 1 model selected  
Alignment identifier is 7/A  

> select #5/A:77

8 atoms, 7 bonds, 1 residue, 1 model selected  
Alignment identifier is 5/A  

> select clear

> color #2 white

> color #5 #ebebebff

> color #7 #d6d6d6ff

> select clear

> select add #2/A:79

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

> select #2/A:80

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

> select #2/A:80-206

996 atoms, 1022 bonds, 127 residues, 1 model selected  

> hide sel cartoons

> select clear

> select add #7/A:109

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

> select #7/A:110

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

> select #7/A:110-291

1411 atoms, 1453 bonds, 182 residues, 1 model selected  

> hide sel cartoons

> select add #5/A:72

1419 atoms, 1460 bonds, 183 residues, 2 models selected  

> select #5/A:73-74

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

> select #5/A:73-346

2090 atoms, 2161 bonds, 274 residues, 1 model selected  

> hide sel cartoons

> select clear

> select add #7

2250 atoms, 2323 bonds, 291 residues, 1 model selected  

> select subtract #7

Nothing selected  

> select add #5

2645 atoms, 2735 bonds, 346 residues, 1 model selected  

> view matrix models
> #5,0.19339,-0.91678,-0.34945,84.461,0.8353,-0.032979,0.5488,1.6976,-0.51465,-0.39803,0.75941,40.18

> view matrix models
> #5,0.19339,-0.91678,-0.34945,84.347,0.8353,-0.032979,0.5488,1.4847,-0.51465,-0.39803,0.75941,40.956

> select clear

> select add #2

1622 atoms, 1672 bonds, 2 pseudobonds, 206 residues, 4 models selected  

> view matrix models
> #2,0.78113,-0.5443,-0.3059,10.914,0.49691,0.83859,-0.22328,20.936,0.37805,0.022403,0.92551,-19.643,#14,1,0,0,0,0,1,0,0,0,0,1,0

> select subtract #2

1 model selected  

> select add #7

2250 atoms, 2323 bonds, 291 residues, 1 model selected  

> select subtract #7

Nothing selected  

> select add #5

2645 atoms, 2735 bonds, 346 residues, 1 model selected  

> view matrix models
> #5,0.19339,-0.91678,-0.34945,78.158,0.8353,-0.032979,0.5488,0.37693,-0.51465,-0.39803,0.75941,37.181

> select clear

> color dark sea green target c

> select clear

> select ::name=""CYS""

1512 atoms, 1391 bonds, 1 pseudobond, 252 residues, 14 models selected  

> show sel & #5,7#!2 atoms

> color sel dark sea green target ac

> select clear

Drag select of 72 atoms, 66 bonds  

> hide sel atoms

Drag select of 12 atoms, 11 bonds  

> hide sel atoms

Drag select of 33 atoms, 32 bonds  

> hide sel atoms

Drag select of 2 atoms, 1 bonds  

> hide sel atoms

Drag select of 1 atoms  

> hide sel atoms

Drag select of 72 atoms, 66 bonds, 2 residues  

> hide sel atoms

> select clear

> hide #!14 models

> hide #14.1 models

> select clear

> color #2,5,7 byhetero

> select clear

> select add #7

2250 atoms, 2323 bonds, 291 residues, 1 model selected  

> select subtract #7

Nothing selected  

> select add #5

2645 atoms, 2735 bonds, 346 residues, 1 model selected  

> view matrix models
> #5,0.19339,-0.91678,-0.34945,73.849,0.8353,-0.032979,0.5488,0.073448,-0.51465,-0.39803,0.75941,34.078

> select clear

> select add #5

2645 atoms, 2735 bonds, 346 residues, 1 model selected  

> select subtract #5

Nothing selected  

> select add #5

2645 atoms, 2735 bonds, 346 residues, 1 model selected  

> select subtract #5

Nothing selected  

> select add #7

2250 atoms, 2323 bonds, 291 residues, 1 model selected  

> view matrix models
> #7,0.29983,0.71847,-0.62762,51.203,-0.28833,-0.55887,-0.77751,-3.9715,-0.90938,0.41408,0.03959,23.115

> select clear

> hide #7 models

> show #7 models

> hide #7 models

> hide #5 models

> select clear

> lighting soft

> select clear

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Stb6-GUB-WAK-
> side.png"" width 911 height 739 supersample 4 transparentBackground true

> hide #!2 models

> show #5 models

> hide #5 models

> show #5 models

> select clear

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Snn1-GUB-WAK-
> side.png"" width 911 height 739 supersample 4 transparentBackground true

> select clear

> hide #5 models

> show #7 models

> select add #7/A:109

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

> hide sel cartoons

> select clear

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Htn1-GUB-WAK-
> side.png"" width 911 height 739 supersample 4 transparentBackground true

> select clear

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Htn1-GUB-WAK-
> top.png"" width 911 height 739 supersample 4 transparentBackground true

> hide #7 models

> show #5 models

> select clear

> show #5 surfaces

> hide #!5 surfaces

> select clear

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Snn1-GUB-WAK-
> top.png"" width 911 height 739 supersample 4 transparentBackground true

> select clear

> show #!2 models

> hide #!5 models

> select clear

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Stb6-GUB-WAK-
> top.png"" width 911 height 739 supersample 4 transparentBackground true

> select clear

> show #!5 models

> show #7 models

> ui tool show Matchmaker

> matchmaker #!5 to #2

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 stb6.pdb, chain A (#2) with
snn1_d97b8_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain A
(#5), sequence alignment score = 78.7  
RMSD between 44 pruned atom pairs is 0.933 angstroms; (across all 166 pairs:
14.577)  
  

> ui tool show Matchmaker

> matchmaker #7 to #2

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 stb6.pdb, chain A (#2) with
Htn1_00234_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain A
(#7), sequence alignment score = 103.3  
RMSD between 69 pruned atom pairs is 0.971 angstroms; (across all 182 pairs:
9.215)  
  

> select clear

> color #5 #ebebebff

> color #5 #009193ff

> color #7 #4f8f00ff

> color #7 #929000ff

> color #7 #009051ff

> color #7 #929000ff

> color #7 #8efa00ff

> color #7 #fffb00ff

> color #7 #73fa79ff

> color #7 #929000ff

> select clear

> color #2 #d4fb79ff

> color #2 #73fa79ff

> color #2 #73fcd6ff

> color #2 #73fa79ff

> color #2 #00f900ff

> color #2 #73fa79ff

> color #2 #00fa92ff

> color #2 #00f900ff

> color #2 #73fa79ff

> select clear

> color #2,5,7 byhetero

> select clear

> select add #2

1622 atoms, 1672 bonds, 2 pseudobonds, 206 residues, 2 models selected  

> color sel light green target ac

> select clear

> color #2,5,7 byhetero

> select clear

> select #2/A:6

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

> select #2/A:6-7

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

> hide sel cartoons

> select #7/A:1

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

> select #7/A:1-2

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

> select clear

> select add #5/A:6

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

> hide sel cartoons

> select clear

> select add #7/A:28

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

> hide sel cartoons

> select clear

> select #2/A:8

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

> select #2/A:8

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

> hide sel cartoons

> select clear

> select add #2

1622 atoms, 1672 bonds, 2 pseudobonds, 206 residues, 2 models selected  

> select add #5

4267 atoms, 4407 bonds, 2 pseudobonds, 552 residues, 4 models selected  

> select add #7

6517 atoms, 6730 bonds, 2 pseudobonds, 843 residues, 6 models selected  

> color sel dark sea green target ac

> select clear

> color #2,5,7 byhetero

> select clear

> hide #!2 models

> show #!2 models

> hide #!5 models

> hide #7 models

> select clear

> show #!5 models

> show #7 models

> hide #!5 models

> hide #7 models

> show #!5 models

> show #7 models

> hide #!5 models

> hide #7 models

> select clear

> show #!5 models

> show #7 models

> hide #!5 models

> hide #7 models

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Stb6-GUB-WAK-
> top.png"" width 911 height 739 supersample 4 transparentBackground true

> show #!5 models

> hide #!2 models

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Snn1-GUB-WAK-
> top.png"" width 911 height 739 supersample 4 transparentBackground true

> select clear

> show #7 models

> hide #!5 models

> show #!5 models

> show #!2 models

> hide #!2 models

> hide #!5 models

> save ""/Users/u6290062/Library/CloudStorage/OneDrive-
> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Htn1-GUB-WAK-
> top.png"" width 911 height 739 supersample 4 transparentBackground true


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

Log:
UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,9
      Model Number: MPHF3X/A
      Chip: Apple M2 Pro
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.140.96
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.6.1 (24G90)
      Kernel Version: Darwin 24.6.0
      Time since boot: 9 days, 2 hours, 33 minutes

Graphics/Displays:

    Apple M2 Pro:

      Chipset Model: Apple M2 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 19
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL S2719H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported
        DELL S2719H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.5.0
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.18
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 2.5.1
    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: 1.6.2
    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: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    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: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    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: 1.1.3
    ChimeraX-ProfileGrids: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    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: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    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: 1.19.1
    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: 2.5.2
    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: 1.45.2
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.9.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.14
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.58.4
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.4.4
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    narwhals: 2.2.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 2.2.6
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    plotly: 6.0.1
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pyKVFinder: 0.8.1
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    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: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tomlkit: 0.13.2
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.0
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14
}}}
"	defect	new	normal		Unassigned