![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 weeks ago
Closed 7 weeks ago
#18674 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
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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"procLaunch" : "2025-08-23 14:53:23.6661 +1000",
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"codeSigningFlags" : 570491649,
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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"
[deleted to fit within ticket limits]
> 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
Change History (2)
comment:1 by , 7 weeks ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 7 weeks ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
Note:
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The ChimeraX crash report panel says what we know about this crash
"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."
The ChimeraX daily build is using a newer Qt version 6.9.1 while ChimeraX 1.10 you were using in this crash uses Qt 6.8.2. Possibly the newer Qt has fixed these Mac multi-display crashes.