id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
20546	Crash on Mac waking from sleep	mimi.mayer@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-26.5-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault

Current thread 0x00000001f4121e80 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 in 
  File """", line 88 in _run_code
  File """", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, openmm._openmm, openmm.app.internal.compiled, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree, chimerax.atom_search.ast (total: 62)


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

> open /Users/mylanmayer/Library/CloudStorage/OneDrive-
> UCSF/Documents/Integrin/Mg_Apo_Extended_Closed/extended_closed_alpha-
> beta_interactions_labeled_v2.cxs

Opened cryosparc_P6_J300_007_volume_map_sharp_z_flip.mrc as #2, grid size
300,300,300, pixel 0.834, shown at level 0.401, step 1, values float32  
Log from Wed Jan 7 14:11:53 2026 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/mylanmayer/Library/CloudStorage/OneDrive-
> UCSF/Desktop/extended_closed_initial_model_ordered_chainA_goodBGOL_real_space_refined_002_isolde_v3.pdb

Chain information for
extended_closed_initial_model_ordered_chainA_goodBGOL_real_space_refined_002_isolde_v3.pdb
#1  
---  
Chain | Description  
A | No description available  
B | No description available  
G | No description available  
L | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
W | No description available  
X | No description available  
Y | No description available  
c | No description available  
f | No description available  
i | No description available  
  

> style stick

Changed 15637 atom styles  

> open
> /Users/mylanmayer/Downloads/cryosparc_P6_J300_007_volume_map_sharp_z_flip.mrc

Opened cryosparc_P6_J300_007_volume_map_sharp_z_flip.mrc as #2, grid size
300,300,300, pixel 0.834, shown at level 0.183, step 2, values float32  

> volume #2 color #bf9fb5

> volume #2 color #bfae74

> volume #2 color #ffe89b

> volume #2 color #ffe5af

> volume #2 color #ffd1d6

> volume #2 step 1

> volume #2 level 0.3579

> volume #2 color #ffd1d676

> volume #2 color #ffd1d675

> open /Users/mylanmayer/Library/CloudStorage/OneDrive-
> UCSF/Desktop/extended_closed_initial_model_ordered_chainA_goodBGOL_real_space_refined_002_isolde_v3.pdb

Chain information for
extended_closed_initial_model_ordered_chainA_goodBGOL_real_space_refined_002_isolde_v3.pdb
#3  
---  
Chain | Description  
A | No description available  
B | No description available  
G | No description available  
L | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
W | No description available  
X | No description available  
Y | No description available  
c | No description available  
f | No description available  
i | No description available  
  

> hide #!1 models

> show #!1 models

> select add #3

15637 atoms, 15784 bonds, 1 pseudobond, 1031 residues, 2 models selected  

> close #1

> select subtract #3

Nothing selected  

> style stick

Changed 15637 atom styles  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 8 residues in model #3 to IUPAC-IUB
standards.  
Chain information for
extended_closed_initial_model_ordered_chainA_goodBGOL_real_space_refined_002_isolde_v3.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/G | No description available  
1.2/L | No description available  
1.2/O | No description available  
1.2/P | No description available  
1.2/Q | No description available  
1.2/R | No description available  
1.2/S | No description available  
1.2/W | No description available  
1.2/X | No description available  
1.2/Y | No description available  
1.2/c | No description available  
1.2/f | No description available  
1.2/i | No description available  
  

> clipper associate #2 toModel #1

Opened cryosparc_P6_J300_007_volume_map_sharp_z_flip.mrc as #1.1.1.1, grid
size 300,300,300, pixel 0.834, shown at step 1, values float32  

> isolde sim start /A-i

ISOLDE: started sim  

> select clear

> volume #1.1.1.1 level 0.6323

> volume #1.1.1.1 level 0.3786

> volume #1.1.1.1 level 0.2676

> volume #1.1.1.1 level 0.2993

> ui mousemode right ""isolde tug residue""

> isolde sim pause

> isolde tutorial

> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  

> st first

> isolde shorthand
    
    
    Registered ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  

> st 775

Unrecognised residue argument! If specified, must be either a residue,
""first"", ""last"", ""next"" or ""prev""  

> st 775

Unrecognised residue argument! If specified, must be either a residue,
""first"", ""last"", ""next"" or ""prev""  

> st #1.2/A:775

[Repeated 1 time(s)]

> isolde sim resume

> volume #1.1.1.1 level 0.2517

> isolde pepflip /A:777

> ui tool show ""Ramachandran Plot""

> isolde pepflip /A:777

> st prev

[Repeated 1 time(s)]

> st

[Repeated 2 time(s)]

> st prev

> isolde pepflip /A:775

> st

> st prev

> isolde pepflip #!1.2/A:775

[Repeated 1 time(s)]

> st prev

> st

[Repeated 1 time(s)]

> isolde pepflip /A:776

[Repeated 1 time(s)]

> isolde cisflip /A:776

[Repeated 1 time(s)]

> st

[Repeated 2 time(s)]

> st prev

[Repeated 3 time(s)]

> isolde pepflip /A:775

> st prev

> st

[Repeated 1 time(s)]

> volume #1.1.1.1 level 0.3469

> st prev

[Repeated 1 time(s)]

> st

[Repeated 2 time(s)]

> isolde pepflip /A:777

[Repeated 1 time(s)]

> isolde cisflip /A:777

[Repeated 1 time(s)]

> isolde pepflip /A:776

[Repeated 1 time(s)]

> isolde pepflip /A:778

[Repeated 4 time(s)]

> isolde pepflip #!1.2/A:779

[Repeated 1 time(s)]

> isolde pepflip /A:780

> volume #1.1.1.1 level 0.3151

> st

[Repeated 1 time(s)]

> '

incomplete quoted text  

> st

[Repeated 5 time(s)]

> volume #1.1.1.1 level 0.2993

> st

> isolde pepflip /A:786

> st prev

> volume #1.1.1.1 level 0.2834

> st

[Repeated 6 time(s)]

> volume #1.1.1.1 level 0.3469

> st

[Repeated 14 time(s)]

> isolde sim pause

> st

> volume #1.1.1.1 level 0.4103

> st

[Repeated 42 time(s)]

> '

incomplete quoted text  

> st

[Repeated 6 time(s)]

> st prev

> ui mousemode right ""isolde tug atom""

> isolde sim resume

> st prev

> st

[Repeated 47 time(s)]

> isolde sim pause

> st

[Repeated 3 time(s)]

> isolde sim resume

> st

[Repeated 2 time(s)]

> ui mousemode right ""isolde tug residue""

> st

[Repeated 19 time(s)]

> ui mousemode right ""isolde tug residue""

[Repeated 1 time(s)]

> ui mousemode right ""isolde tug atom""

> st

[Repeated 2 time(s)]

> isolde sim pause

> st

[Repeated 13 time(s)]

> st #1.2/A:775

> st \

Unrecognised residue argument! If specified, must be either a residue,
""first"", ""last"", ""next"" or ""prev""  

> st

[Repeated 1 time(s)]

> isolde sim resume

> isolde sim pause

> isolde sim resume

> isolde pepflip /A:779

> isolde pepflip /A:778

> isolde cisflip /A:779

> st

> st prev

> volume #1.1.1.1 level 0.3469

> isolde pepflip /A:776

[Repeated 1 time(s)]

> isolde cisflip /A:776

[Repeated 1 time(s)]

> isolde cisflip /A:777

[Repeated 1 time(s)]

> isolde pepflip #!1.2/A:779

[Repeated 1 time(s)]

> st prev

> isolde sim pause

> save /Users/mylanmayer/Library/CloudStorage/OneDrive-
> UCSF/Desktop/extended_closed_initial_model_ordered_chainA_goodBGOL_real_space_refined_002_isolde_v4.pdb

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 5 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> close

> open /Users/mylanmayer/Library/CloudStorage/OneDrive-
> UCSF/Desktop/extended_closed_initial_model_ordered_chainA_goodBGOL_real_space_refined_002_isolde_v4.pdb

Chain information for
extended_closed_initial_model_ordered_chainA_goodBGOL_real_space_refined_002_isolde_v4.pdb
#1  
---  
Chain | Description  
A | No description available  
B | No description available  
G | No description available  
L | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
W | No description available  
X | No description available  
Y | No description available  
c | No description available  
f | No description available  
i | No description available  
  

> style stick

Changed 15637 atom styles  

> open /Users/mylanmayer/Library/CloudStorage/OneDrive-
> UCSF/Desktop/extended_closed_initial_model_ordered_chainA_goodBGOL_real_space_refined_002_isolde_v4.pdb
> format pdb

Chain information for
extended_closed_initial_model_ordered_chainA_goodBGOL_real_space_refined_002_isolde_v4.pdb
#2  
---  
Chain | Description  
A | No description available  
B | No description available  
G | No description available  
L | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
W | No description available  
X | No description available  
Y | No description available  
c | No description available  
f | No description available  
i | No description available  
  

> style stick

Changed 31274 atom styles  

> select add #2

15637 atoms, 15784 bonds, 1 pseudobond, 1031 residues, 2 models selected  

> close #2

> open
> /Users/mylanmayer/Downloads/cryosparc_P6_J300_007_volume_map_sharp_z_flip.mrc

Opened cryosparc_P6_J300_007_volume_map_sharp_z_flip.mrc as #2, grid size
300,300,300, pixel 0.834, shown at level 0.183, step 2, values float32  

> volume #2 step 1

> volume #2 level 0.3676

> label #1-2 attribute name

> ~label #1-2 atoms

> ~label #1-2 residues

> ui tool show ""Change Chain IDs""

> select O

1569 atoms, 1031 residues, 1 model selected  

> hide #!2 models

> select clear

> select /L

284 atoms, 286 bonds, 22 residues, 1 model selected  

> select /O

721 atoms, 725 bonds, 46 residues, 1 model selected  

> select /B

4445 atoms, 4490 bonds, 285 residues, 1 model selected  

> select clear

> select /L,O

1005 atoms, 1013 bonds, 68 residues, 1 model selected  

> select /L,O,B

5450 atoms, 5503 bonds, 353 residues, 1 model selected  

> select /L,O,B,G

6585 atoms, 6646 bonds, 427 residues, 1 model selected  

> select /L,O,B,B

5450 atoms, 5503 bonds, 353 residues, 1 model selected  

> select /L,O,B,G

6585 atoms, 6646 bonds, 427 residues, 1 model selected  

> select /L,O,B,G,D

6585 atoms, 6646 bonds, 427 residues, 1 model selected  

> select /L,O,B,G,D,N

6585 atoms, 6646 bonds, 427 residues, 1 model selected  

> ui tool show ""Change Chain IDs""

> changechains sel B

Proposed chain ID change would produce multiple residues with the samechain-
ID/number/insertion-code combo (B/4/)  

> select /L,O,B,G,D,N

6585 atoms, 6646 bonds, 427 residues, 1 model selected  

> ui tool show ""Change Chain IDs""

> ui tool show ""Show Sequence Viewer""

> ui tool show ""Change Chain IDs""

> changechains sel z

Proposed chain ID change would produce multiple residues with the samechain-
ID/number/insertion-code combo (z/7/)  

> show #!2 models

> color #2 #b2b2b274 models

> color #2 #bf8e7474 models

> color #2 #bf8e7475 models

> set bgColor white

> ui mousemode right zoom

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> volume #2 level 0.2166

> volume #2 level 0.4011

> color sel byhetero

> select H

7723 atoms, 1031 residues, 1 model selected  

> hide sel target a

> ui mousemode right translate

> select /L,O,B,G,D,N

6585 atoms, 6646 bonds, 427 residues, 1 model selected  

> color sel red

> select clear

> select /A

8399 atoms, 8492 bonds, 1 pseudobond, 556 residues, 2 models selected  

> color (#!1 & sel) cornflower blue

> select clear

> hide #!1 models

> show #!1 models

> hide #!2 models

> open /Users/mylanmayer/Library/CloudStorage/OneDrive-
> UCSF/Documents/Integrin/bent_model_9-19-25.pdb

Chain information for bent_model_9-19-25.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
  

> style stick

Changed 27059 atom styles  

> hide #!1 models

> select /L,O,B,G,D,N

10660 atoms, 10783 bonds, 958 residues, 2 models selected  

> color (#!3 & sel) orange

> color (#!3 & sel) orange red

> color (#!3 & sel) orange

> select /F,J,C,A,I,E,K,M,H

14970 atoms, 15187 bonds, 4 pseudobonds, 1415 residues, 4 models selected  

> color (#!3 & sel) cyan

> select clear

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!3 models

> select #1/B:223@CD

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:551@CG

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:217@CB

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:523@CD

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:195@CG

1 atom, 1 residue, 1 model selected  

> select #1/B:195@CD

1 atom, 1 residue, 1 model selected  

> select #1/B:195@CG

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:617@CZ

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:47@CD

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:641@CZ

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:194@CG

1 atom, 1 residue, 1 model selected  

> color sel dim gray

Drag select of 16 atoms, 15 bonds  

> select clear

> select #1/A:50@CZ

1 atom, 1 residue, 1 model selected  
Drag select of 2 bonds  

> select clear

> select #1/A:50@CZ

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:193@CB

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:188@CE

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:212@CZ

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:76@CZ

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:190@C

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:69@CH2

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:191@C

1 atom, 1 residue, 1 model selected  

> color sel dim gray

[Repeated 1 time(s)]

> select #1/B:191@C

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:92@SD

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:378@SD

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:404@CZ2

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:517@SD

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:250@CG

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:487@CG1

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:218@CB

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:219@CA

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:461@CZ

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:181@C

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:490@CZ

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:184@C

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:436@CZ

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:145@CG

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:142@CD

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:96@CB

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:98@CB

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:143@CE2

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:140@C

1 atom, 1 residue, 1 model selected  

> select #1/A:138@CD

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:141@CG

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:101@CE

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:439@CZ

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:185@C

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:383@CE1

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:189@CG

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:399@CB

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:374@CZ

1 atom, 1 residue, 1 model selected  

> select #1/B:144@CG

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:434@CB

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:146@CB

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:553@CZ

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:184@CA

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select /A:76

28 atoms, 26 bonds, 2 residues, 2 models selected  

> select /B:92

25 atoms, 23 bonds, 2 residues, 2 models selected  

> save /Users/mylanmayer/Documents/Integrin/extended_closed_alpha-
> beta_interactions_labeled.cxs

> select clear

> select #1/A:432@C

1 atom, 1 residue, 1 model selected  
Drag select of 2 bonds  

> select clear

> select #1/A:432@C

1 atom, 1 residue, 1 model selected  

> select #1/A:432@CG

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:239@CD

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:521@CE

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:250@C

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:486@CD

1 atom, 1 residue, 1 model selected  

> select #1/A:487@CD1

1 atom, 1 residue, 1 model selected  

> select add #1/B:246@OE1

2 atoms, 2 residues, 1 model selected  

> ui tool show Distances

> ui mousemode right zoom

> ui mousemode right clip

[Repeated 1 time(s)]

> ui mousemode right zoom

> save /Users/mylanmayer/Documents/Integrin/extended_closed_alpha-
> beta_interactions_labeled_v2.cxs

——— End of log from Wed Jan 7 14:11:53 2026 ———

opened ChimeraX session  

> ui tool show ""Side View""

> ui tool show Contacts

Drag select of 564 atoms, 1 pseudobonds, 579 bonds  
Drag select of 1073 atoms, 1 pseudobonds, 1099 bonds  

> contacts sel restrict both distanceOnly 3.5 resSeparation 5 intraMol false
> ignoreHiddenModels true reveal true

40 distances  

> ui mousemode right zoom

> ui mousemode right translate

> select clear

> ui mousemode right zoom

> ui mousemode right translate

> select add #1

15637 atoms, 15784 bonds, 41 pseudobonds, 1031 residues, 3 models selected  

> color sel byhetero

> select subtract #1

Nothing selected  

> ui mousemode right zoom

> ui mousemode right translate

> ui mousemode right zoom

> ui mousemode right translate

> ui mousemode right zoom

> ui mousemode right translate

> select add #1

15637 atoms, 15784 bonds, 41 pseudobonds, 1031 residues, 3 models selected  

> select subtract #1

Nothing selected  

> select add #1

15637 atoms, 15784 bonds, 41 pseudobonds, 1031 residues, 3 models selected  

> show sel cartoons

> hide sel atoms

> select subtract #1

Nothing selected  


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

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

> open
> /Volumes/4_IND_EM/southworth_lab/mmayer/processing/mmayer_20260204_TgM83-1_homo/relion/Class3D/selected_singlets_singlet-2_initial_model/run_it050_class003.mrc

Opened run_it050_class003.mrc as #1, grid size 288,288,288, pixel 0.728, shown
at level 0.0034, step 2, values float32  

> open
> /Volumes/4_IND_EM/southworth_lab/mmayer/processing/mmayer_20260204_TgM83-1_homo/relion/Class3D/selected_singlets_singlet-2_initial_model/run_it050_class002.mrc

Opened run_it050_class002.mrc as #2, grid size 288,288,288, pixel 0.728, shown
at level 0.00709, step 2, values float32  

> open
> /Volumes/4_IND_EM/southworth_lab/mmayer/processing/mmayer_20260204_TgM83-1_homo/relion/Class3D/selected_singlets_singlet-2_initial_model/run_it050_class001.mrc

Opened run_it050_class001.mrc as #3, grid size 288,288,288, pixel 0.728, shown
at level 0.00677, step 2, values float32  

> ui tool show Registration




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac15,6
      Model Number: MRX73LL/A
      Chip: Apple M3 Pro
      Total Number of Cores: 12 (6 Performance and 6 Efficiency)
      Memory: 18 GB
      System Firmware Version: 18000.120.36
      OS Loader Version: 18000.120.36

Software:

    System Software Overview:

      System Version: macOS 26.5 (25F71)
      Kernel Version: Darwin 25.5.0
      Time since boot: 30 days, 1 hour, 1 minute

Graphics/Displays:

    Apple M3 Pro:

      Chipset Model: Apple M3 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 18
      Vendor: Apple (0x106b)
      Metal Support: Metal 4
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        DELL P2424HEB:
          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
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    autocommand: 2.2.2
    babel: 2.16.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-Clipper: 0.24.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ISOLDE: 1.9
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    importlib_metadata: 8.0.0
    importlib_resources: 6.4.0
    inflect: 7.3.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    more-itertools: 10.3.0
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    ordered-set: 4.1.0
    packaging: 23.2
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    platformdirs: 4.2.2
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4.2
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing_extensions: 4.12.2
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    zipp: 3.19.2
}}}
"	defect	closed	normal		Window Toolkit		duplicate						all	ChimeraX