id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
19287	mshMIGPerform crash in NSAccessiblity native Mac APIs	chimerax-bug-report@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-15.7.1-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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        ""SIRI_HOME_AUTOMATION_INTENT_SELECTION_CACHE"" : ""642600a457e7664b1698eb32""
      },
      ""deploymentId"" : 240000004
    }
  ],
  ""experiments"" : [

  ]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open ""/Users/zang/Postdoc/Ablasser/TIR/STING-TIR
> chimera/SfSTING(7UN8)_SARM1TIR(7NAK)_TLR5TIR(3J0A)/SfSTING(7UN8)_TLR5TIR(3J0A)_SARM1TIR(7NAK).cxs""

Log from Sun Nov 2 15:17:32 2025UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/zang/Downloads/structures_2025-10-29-14-28-45/7NAK.A.cif

Summary of feedback from opening
/Users/zang/Downloads/structures_2025-10-29-14-28-45/7NAK.A.cif  
---  
note | PDBx/mmCIF styling lost on line 12784. Rereading mmCIF file from the beginning.  
  
7NAK.A.cif title:  
Cryo-EM structure of activated human SARM1 in complex with NMN and 1AD
(TIR:1AD) [more info...]  
  
Chain information for 7NAK.A.cif #1  
---  
Chain | Description | UniProt  
A B C D E F G H | NAD(+) hydrolase SARM1 | SARM1_HUMAN 28-724  
  
Non-standard residues in 7NAK.A.cif #1  
---  
1QD —
[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-
oxidanyl-phosphoryl]
[(2~{R},3~{S},4~{R},5~{R})-5-(5-iodanylisoquinolin-2-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl
hydrogen phosphate  
  

> open /Users/zang/Downloads/structures_2025-10-29-14-28-45/7UN8.A.cif

Summary of feedback from opening
/Users/zang/Downloads/structures_2025-10-29-14-28-45/7UN8.A.cif  
---  
note | PDBx/mmCIF styling lost on line 4588. Rereading mmCIF file from the beginning.  
  
7UN8.A.cif title:  
SfSTING with c-di-GMP single fiber [more info...]  
  
Chain information for 7UN8.A.cif #2  
---  
Chain | Description | UniProt  
A B C D E F | CD-NTase-associated protein 12 | CAP12_SPHFK 2-323  
  
Non-standard residues in 7UN8.A.cif #2  
---  
C2E —
9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)
(c-di-GMP;Cyclic diguanosine monophosphate)  
  

> select add #1

18367 atoms, 18615 bonds, 1128 residues, 1 model selected  

> select add #2

32434 atoms, 32916 bonds, 18 pseudobonds, 2911 residues, 3 models selected  

> hide sel atoms

> show sel cartoons

> select subtract #1

14067 atoms, 14301 bonds, 18 pseudobonds, 1783 residues, 2 models selected  

> select subtract #2

Nothing selected  

> hide #1 models

> show #1 models

> hide #2.1 models

> show #2.1 models

> hide #2.1 models

> show #2.1 models

Drag select of 126 residues  

> select clear

> select #2/B:2-322

2324 atoms, 2360 bonds, 3 pseudobonds, 297 residues, 2 models selected  

> select #2/C:2-322

2315 atoms, 2351 bonds, 3 pseudobonds, 296 residues, 2 models selected  

> select #2/D:2-322

2324 atoms, 2360 bonds, 3 pseudobonds, 297 residues, 2 models selected  

> select #2/E:2-322

2318 atoms, 2354 bonds, 3 pseudobonds, 296 residues, 2 models selected  

> select #2/F:2-322

2324 atoms, 2360 bonds, 3 pseudobonds, 297 residues, 2 models selected  

> select #2/A:2-322

2324 atoms, 2360 bonds, 3 pseudobonds, 297 residues, 2 models selected  

> help help:user

> select #2/A:2-120

881 atoms, 892 bonds, 1 pseudobond, 114 residues, 2 models selected  

> show #1 target m

> select clear

> select #2/A:2-120

881 atoms, 892 bonds, 1 pseudobond, 114 residues, 2 models selected  

> cartoon (#!2 & sel)

> select ~sel & ##selected

13186 atoms, 13409 bonds, 17 pseudobonds, 1669 residues, 2 models selected  

> transparency ##selected 50 ribbons

> select clear

> select /A:561-700

2242 atoms, 2268 bonds, 140 residues, 1 model selected  

> select /A:561-700

2242 atoms, 2268 bonds, 140 residues, 1 model selected  

> select /A:561-700

2242 atoms, 2268 bonds, 140 residues, 1 model selected  

> select /B:561-700

2243 atoms, 2269 bonds, 140 residues, 1 model selected  

> select /C:561-700

2242 atoms, 2268 bonds, 140 residues, 1 model selected  

> select /D:561-700

2243 atoms, 2269 bonds, 140 residues, 1 model selected  

> undo

[Repeated 9 time(s)]

> transparency ##selected 0 ribbons

> select #2/A:121-322

1443 atoms, 1468 bonds, 1 pseudobond, 183 residues, 2 models selected  

> select #2/A:2-120

881 atoms, 892 bonds, 1 pseudobond, 114 residues, 2 models selected  

> select ~sel & ##selected

13186 atoms, 13409 bonds, 17 pseudobonds, 1669 residues, 2 models selected  

> transparency ##selected 70 ribbons

> undo

[Repeated 2 time(s)]

> transparency ##selected 0 ribbons

> transparency ##selected 70 ribbons

> transparency #2/A:2-120 0 ribbons

> select clear

> select #1/d

2297 atoms, 2328 bonds, 141 residues, 1 model selected  

> select ~sel & ##selected

16070 atoms, 16287 bonds, 987 residues, 1 model selected  

> transparency ##selected 70 ribbons

> transparency #1/D 0 ribbons

> select clear

> save ""/Users/zang/Postdoc/Ablasser/TIR/Structure
> superimposition/SARM1-TIR(7NAK)_SfSTING-TIR(7UN8) .cxs""

> select :1QD

432 atoms, 472 bonds, 8 residues, 1 model selected  

> select :1QD

432 atoms, 472 bonds, 8 residues, 1 model selected  

> show sel atoms

Unsupported scale factor (0.000000) detected on Display0  

[Repeated 3 time(s)]

Unsupported scale factor (0.000000) detected on Display1  

[Repeated 44 time(s)]

Unsupported scale factor (0.000000) detected on Display0  

[Repeated 2 time(s)]

Unsupported scale factor (0.000000) detected on Display1  

[Repeated 2 time(s)]

> select clear

> select #2/D:2-322

2324 atoms, 2360 bonds, 3 pseudobonds, 297 residues, 2 models selected  

> select #2/A:2-120

881 atoms, 892 bonds, 1 pseudobond, 114 residues, 2 models selected  

> split #2/A atoms:2-120

Expected a keyword  

> split #2/A atoms : 2-120 atoms : 121-322

Split 7UN8.A.cif (#2) into 3 models  
Chain information for 7UN8.A.cif 1 #2.1  
---  
Chain | Description  
A B D F | No description available  
C | No description available  
E | No description available  
  
Chain information for 7UN8.A.cif 2 #2.2  
---  
Chain | Description  
A B C D E F | No description available  
  

> hide #!2.1 models

> hide #!2.2 models

> hide #2.3 models

> show #!2.1 models

> hide #!2.1 models

> show #!2.1 models

> hide #!2.1 models

> show #!2.1 models

> hide #!2.1 models

> show #!2.1 models

> hide #!2.1 models

> show #!2.2 models

> hide #!2.2 models

> show #2.3 models

> hide #2.3 models

> show #2.3 models

> hide #2.3 models

> show #2.3 models

> hide #2.3 models

> show #!2.1 models

> hide #!2.1 models

> show #!2.1 models

> show #!2.2 models

> hide #!2.1 models

> hide #!2.2 models

> split #2.1

Split 7UN8.A.cif 1 (#2.1) into 6 models  
Chain information for 7UN8.A.cif 1 A #2.1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 7UN8.A.cif 1 B #2.1.2  
---  
Chain | Description  
B | No description available  
  
Chain information for 7UN8.A.cif 1 C #2.1.3  
---  
Chain | Description  
C | No description available  
  
Chain information for 7UN8.A.cif 1 D #2.1.4  
---  
Chain | Description  
D | No description available  
  
Chain information for 7UN8.A.cif 1 E #2.1.5  
---  
Chain | Description  
E | No description available  
  
Chain information for 7UN8.A.cif 1 F #2.1.6  
---  
Chain | Description  
F | No description available  
  

> hide #!2.1 models

> show #!2.1 models

> hide #!2.1 models

> show #!2.1 models

> hide #!2.1 models

> show #!2.1 models

> hide #!2.1 models

> show #!2.1 models

> hide #!2.1 models

> select add #2.1

5271 atoms, 5337 bonds, 6 pseudobonds, 682 residues, 13 models selected  

> select subtract #2.1

Nothing selected  

> show #!2.1.1 models

> split #1

Split 7NAK.A.cif (#1) into 8 models  
Chain information for 7NAK.A.cif A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 7NAK.A.cif B #1.2  
---  
Chain | Description  
B | No description available  
  
Chain information for 7NAK.A.cif C #1.3  
---  
Chain | Description  
C | No description available  
  
Chain information for 7NAK.A.cif D #1.4  
---  
Chain | Description  
D | No description available  
  
Chain information for 7NAK.A.cif E #1.5  
---  
Chain | Description  
E | No description available  
  
Chain information for 7NAK.A.cif F #1.6  
---  
Chain | Description  
F | No description available  
  
Chain information for 7NAK.A.cif G #1.7  
---  
Chain | Description  
G | No description available  
  
Chain information for 7NAK.A.cif H #1.8  
---  
Chain | Description  
H | No description available  
  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> select add #1

18367 atoms, 18615 bonds, 1128 residues, 9 models selected  

> hide #!1 models

> show #!1 models

> select subtract #1

Nothing selected  

> select add #1

18367 atoms, 18615 bonds, 1128 residues, 9 models selected  

> hide #!1 target m

[Repeated 1 time(s)]

> select subtract #1

Nothing selected  

> show #!1 models

> hide #1.1-8 target m

> show #1.4 models

> hide #!2.1.1 models

> show #!2.1.1 models

> hide #!2.1.1 models

> show #!2.1.1 models

> hide #!2.1.1 models

> show #!2.1.1 models

> hide #!2.1.1 models

> show #!2.1.1 models

> hide #1.4 models

> show #1.4 models

> hide #1.4 models

> show #1.4 models

> split #2.2

Split 7UN8.A.cif 2 (#2.2) into 6 models  
Chain information for 7UN8.A.cif 2 A #2.2.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 7UN8.A.cif 2 B #2.2.2  
---  
Chain | Description  
B | No description available  
  
Chain information for 7UN8.A.cif 2 C #2.2.3  
---  
Chain | Description  
C | No description available  
  
Chain information for 7UN8.A.cif 2 D #2.2.4  
---  
Chain | Description  
D | No description available  
  
Chain information for 7UN8.A.cif 2 E #2.2.5  
---  
Chain | Description  
E | No description available  
  
Chain information for 7UN8.A.cif 2 F #2.2.6  
---  
Chain | Description  
F | No description available  
  

> show #!2.2.1 models

> select clear

> save ""/Users/zang/Postdoc/Ablasser/TIR/Structure
> superimposition/SARM1-TIR(7NAK)_SfSTING-TIR(7UN8) .cxs""

> show #2.3 models

> hide #2.3 models

> show #2.3 models

> hide #2.3 models

> show #!2.1.2 models

> show #!2.2.2 models

> show #!2.2.3 models

> hide #!2.2.3 models

> show #!2.1.3 models

> hide #!2.1.3 models

> show #!2.1.4 models

> show #!2.2.4 models

> show #!2.1.3 models

> hide #!2.1.4 models

> show #!2.2.3 models

> hide #!2.2.4 models

> hide #!2.1.2 models

> hide #!2.1.3 models

> hide #!2.2.2 models

> show #!2.2.4 models

> hide #!2.2.3 models

> hide #!2.2.4 models

> show #!2.2.2 models

> hide #!2.2.2 models

> show #!2.2.2 models

> hide #!2.2.2 models

> show #!2.1.2 models

> select #2.2.1/A:136

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

> show sel atoms

> style sel stick

Changed 8 atom styles  

> select #1.4/D:695

19 atoms, 18 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 19 atom styles  

> show sel atoms

> style sel stick

Changed 19 atom styles  

> style sel stick

Changed 19 atom styles  

> show (sel-residues & sidechain) target ab

> hide sel atoms

> show sel atoms

> style sel sphere

Changed 19 atom styles  

> style sel stick

Changed 19 atom styles  

> label sel atoms attribute element

> undo

> ~label sel atoms

> style sel stick

Changed 19 atom styles  

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

> cartoon hide sel-residues

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

> show sel cartoons

> show sel atoms

> select H

9031 atoms, 1128 residues, 8 models selected  

> hide sel & #1.4 atoms

> select clear

> select #1.4/D:696

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1.4/D:693

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

> show sel atoms

> style sel stick

Changed 15 atom styles  

> select H

9031 atoms, 1128 residues, 8 models selected  

> hide sel & #1.4 atoms

> select clear

> select #2.2.1/A:134

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

> show sel atoms

> style sel stick

Changed 9 atom styles  

> select clear

> select #1.4/D:699

19 atoms, 18 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel stick

Changed 19 atom styles  

> select H

9031 atoms, 1128 residues, 8 models selected  

> hide sel & #1.4 atoms

> select #2.2.1/A:140

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

> show sel atoms

> style sel stick

Changed 8 atom styles  

> save ""/Users/zang/Postdoc/Ablasser/TIR/Structure
> superimposition/SARM1-TIR(7NAK)_SfSTING-TIR(7UN8) .cxs""

> select #2.1.1/A:118

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

> show sel atoms

> style sel stick

Changed 9 atom styles  

> select #1.4/D:682

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

> show sel atoms

> style sel stick

Changed 22 atom styles  

> select H

9031 atoms, 1128 residues, 8 models selected  

> hide sel & #1.4 atoms

> select clear

> show #!2.1.3 models

> show #!2.1.4 models

> show #!2.1.5 models

> show #2.3 models

> hide #2.3 models

> show #2.3 models

> hide #2.3 models

> show #2.3 models

> hide #2.3 models

> show #2.3 models

> hide #2.3 models

> hide #!2 models

> show #!2 models

> hide #!2.2 models

> hide #!2.1 models

> show #2.3 models

> hide #2.3 models

> show #!2.1 models

> show #!2.2 models

> show #1.5 models

> hide #1.5 models

> show #1.6 models

> hide #1.6 models

> show #1.3 models

> hide #1.3 models

> show #1.1 models

> hide #1.1 models

> show #1.2 models

> show #1.1 models

> show #1.3 models

> show #1.5 models

> show #1.6 models

> show #1.7 models

> show #1.8 models

> hide #1.1 models

> hide #1.2 models

> hide #1.3 models

> hide #1.4 models

> hide #1.5 models

> show #1.5 models

> hide #1.5 models

> show #1.4 models

> hide #1.6 models

> hide #1.7 models

> hide #1.8 models

> show #1.1 models

> hide #1.1 models

> show #1.3 models

> hide #1.3 models

> show #1.3 models

> show #1.5 models

> hide #1.5 models

> show #1.6 models

> hide #1.6 models

> show #1.7 models

> hide #1.3 models

> hide #1.4 models

> show #1.4 models

> hide #1.4 models

> show #1.4 models

> hide #!2.1.2 models

> show #!2.1.2 models

> hide #!2.1.2 models

> show #!2.1.2 models

> hide #!2.1.3 models

> show #!2.1.3 models

> hide #!2.1.4 models

> hide #!2.1.5 models

> show #!2.1.4 models

> hide #!2.1.4 models

> show #!2.2.2 models

> show #!2.2.3 models

> hide #!2.2.2 models

> save ""/Users/zang/Postdoc/Ablasser/TIR/Structure
> superimposition/SARM1-TIR(7NAK)_SfSTING-TIR(7UN8) .cxs""

> close session

> open
> /Users/zang/Downloads/fold_2025_10_29_14_21_tlr4x2/fold_2025_10_29_14_21_tlr4x2_model_0.cif

Chain information for fold_2025_10_29_14_21_tlr4x2_model_0.cif #1  
---  
Chain | Description  
A B | .  
  
Computing secondary structure  

> open
> /Users/zang/Downloads/fold_2025_10_29_14_21_tlr4x2/fold_2025_10_29_14_21_tlr4x2_model_1.cif

Chain information for fold_2025_10_29_14_21_tlr4x2_model_1.cif #2  
---  
Chain | Description  
A B | .  
  

> open
> /Users/zang/Downloads/fold_2025_10_29_14_21_tlr4x2/fold_2025_10_29_14_21_tlr4x2_model_2.cif

Chain information for fold_2025_10_29_14_21_tlr4x2_model_2.cif #3  
---  
Chain | Description  
A B | .  
  

> open
> /Users/zang/Downloads/fold_2025_10_29_14_21_tlr4x2/fold_2025_10_29_14_21_tlr4x2_model_3.cif

Chain information for fold_2025_10_29_14_21_tlr4x2_model_3.cif #4  
---  
Chain | Description  
A B | .  
  

> open
> /Users/zang/Downloads/fold_2025_10_29_14_21_tlr4x2/fold_2025_10_29_14_21_tlr4x2_model_4.cif

Chain information for fold_2025_10_29_14_21_tlr4x2_model_4.cif #5  
---  
Chain | Description  
A B | .  
  
Computing secondary structure  
[Repeated 3 time(s)]

> hide #1 models

> hide #2 models

> hide #3 models

> hide #4 models

> hide #5 models

> show #1 models

> hide #1 models

> show #2 models

> show #1 models

> hide #1 models

> hide #2 models

> show #1 models

> hide #1 models

> show #2 models

> hide #2 models

> show #3 models

> hide #3 models

> show #2 models

> hide #2 models

> show #1 models

> hide #1 models

> show #4 models

> hide #4 models

> show #5 models

> hide #5 models

> close session

> open ""/Users/zang/Postdoc/Ablasser/TIR/STING-TIR
> chimera/SfSTING(7UN8)_SARM1TIR(7NAK)_TLR4TIR_structures_2025-10-31-15-56-8/4e1e239d7615b4f2.A.cif""
> ""/Users/zang/Postdoc/Ablasser/TIR/STING-TIR
> chimera/SfSTING(7UN8)_SARM1TIR(7NAK)_TLR4TIR_structures_2025-10-31-15-56-8/7NAK.A.cif""
> ""/Users/zang/Postdoc/Ablasser/TIR/STING-TIR
> chimera/SfSTING(7UN8)_SARM1TIR(7NAK)_TLR4TIR_structures_2025-10-31-15-56-8/7UN8.A.cif""

Summary of feedback from opening /Users/zang/Postdoc/Ablasser/TIR/STING-TIR
chimera/SfSTING(7UN8)_SARM1TIR(7NAK)_TLR4TIR_structures_2025-10-31-15-56-8/7NAK.A.cif  
---  
note | PDBx/mmCIF styling lost on line 12768. Rereading mmCIF file from the beginning.  
  
Summary of feedback from opening /Users/zang/Postdoc/Ablasser/TIR/STING-TIR
chimera/SfSTING(7UN8)_SARM1TIR(7NAK)_TLR4TIR_structures_2025-10-31-15-56-8/7UN8.A.cif  
---  
note | PDBx/mmCIF styling lost on line 4604. Rereading mmCIF file from the beginning.  
  
Chain information for 4e1e239d7615b4f2.A.cif #1  
---  
Chain | Description  
A B | .  
  
7NAK.A.cif title:  
Cryo-EM structure of activated human SARM1 in complex with NMN and 1AD
(TIR:1AD) [more info...]  
  
Chain information for 7NAK.A.cif #2  
---  
Chain | Description | UniProt  
A B C D E F G H | NAD(+) hydrolase SARM1 | SARM1_HUMAN 28-724  
  
Non-standard residues in 7NAK.A.cif #2  
---  
1QD —
[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-
oxidanyl-phosphoryl]
[(2~{R},3~{S},4~{R},5~{R})-5-(5-iodanylisoquinolin-2-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl
hydrogen phosphate  
  
7UN8.A.cif title:  
SfSTING with c-di-GMP single fiber [more info...]  
  
Chain information for 7UN8.A.cif #3  
---  
Chain | Description | UniProt  
A B C D E F | CD-NTase-associated protein 12 | CAP12_SPHFK 2-323  
  
Non-standard residues in 7UN8.A.cif #3  
---  
C2E —
9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)
(c-di-GMP;Cyclic diguanosine monophosphate)  
  
Computing secondary structure  

> hide atoms

> show cartoons

> save ""/Users/zang/Postdoc/Ablasser/TIR/STING-TIR
> chimera/SfSTING(7UN8)_SARM1TIR(7NAK)_TLR4TIR_structures_2025-10-31-15-56-8/SfSTING(7UN8)_TLR4TIR_SARM1TIR(7NAK).cxs""

> split #1

Split 4e1e239d7615b4f2.A.cif (#1) into 2 models  
Chain information for 4e1e239d7615b4f2.A.cif A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 4e1e239d7615b4f2.A.cif B #1.2  
---  
Chain | Description  
B | No description available  
  

> split #2

Split 7NAK.A.cif (#2) into 8 models  
Chain information for 7NAK.A.cif A #2.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 7NAK.A.cif B #2.2  
---  
Chain | Description  
B | No description available  
  
Chain information for 7NAK.A.cif C #2.3  
---  
Chain | Description  
C | No description available  
  
Chain information for 7NAK.A.cif D #2.4  
---  
Chain | Description  
D | No description available  
  
Chain information for 7NAK.A.cif E #2.5  
---  
Chain | Description  
E | No description available  
  
Chain information for 7NAK.A.cif F #2.6  
---  
Chain | Description  
F | No description available  
  
Chain information for 7NAK.A.cif G #2.7  
---  
Chain | Description  
G | No description available  
  
Chain information for 7NAK.A.cif H #2.8  
---  
Chain | Description  
H | No description available  
  

> split #3

Split 7UN8.A.cif (#3) into 6 models  
Chain information for 7UN8.A.cif A #3.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 7UN8.A.cif B #3.2  
---  
Chain | Description  
B | No description available  
  
Chain information for 7UN8.A.cif C #3.3  
---  
Chain | Description  
C | No description available  
  
Chain information for 7UN8.A.cif D #3.4  
---  
Chain | Description  
D | No description available  
  
Chain information for 7UN8.A.cif E #3.5  
---  
Chain | Description  
E | No description available  
  
Chain information for 7UN8.A.cif F #3.6  
---  
Chain | Description  
F | No description available  
  

> hide #!3 models

> hide #!2 models

> hide #2.1-8 target m

> show #2.1 models

> hide #2.1 models

> show #2.2 models

> hide #2.2 models

> show #2.4 models

> hide #2.4 models

> hide #!3.1-6 target m

> show #!3.1 models

> split #1.1 atoms : 1-671

Split 4e1e239d7615b4f2.A.cif A (#1.1) into 2 models  
Chain information for 4e1e239d7615b4f2.A.cif A 1 #1.1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 4e1e239d7615b4f2.A.cif A 2 #1.1.2  
---  
Chain | Description  
A | No description available  
  

> hide #1.1.1 models

> split #1.2 atoms : 1-671

Split 4e1e239d7615b4f2.A.cif B (#1.2) into 2 models  
Chain information for 4e1e239d7615b4f2.A.cif B 1 #1.2.1  
---  
Chain | Description  
B | No description available  
  
Chain information for 4e1e239d7615b4f2.A.cif B 2 #1.2.2  
---  
Chain | Description  
B | No description available  
  

> hide #1.2.1 models

> split #3.1 atoms : 146-322

Split 7UN8.A.cif A (#3.1) into 2 models  
Chain information for 7UN8.A.cif A 1 #3.1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 7UN8.A.cif A 2 #3.1.2  
---  
Chain | Description  
A | No description available  
  

> hide #!3.1.1 models

> show #!3.2 models

> hide #!3.2 models

> show #!3.2 models

> show #!3.1.1 models

> hide #!1 models

> hide #!3 models

> show #2.4 models

> show #!1 models

> show #2.3 models

> select :1QD

432 atoms, 472 bonds, 8 residues, 8 models selected  

> show sel & #2.3-4 atoms

> select add #2.3

2674 atoms, 2740 bonds, 148 residues, 8 models selected  

> select subtract #2.3

378 atoms, 413 bonds, 7 residues, 7 models selected  

> select add #2.4

2621 atoms, 2682 bonds, 147 residues, 7 models selected  

> color (#2.4 & sel) lime

> color (#2.4 & sel) cornflower blue

> select add #2.3

4917 atoms, 5009 bonds, 288 residues, 8 models selected  

> color (#2.3-4 & sel) light sea green

> select clear

> select :1QD

432 atoms, 472 bonds, 8 residues, 8 models selected  

> color (#2.3-4 & sel) byhetero

> select clear

> hide #!2 models

> show #1.1.1 models

> show #1.2.1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3.1.2 models

> show #!3.1.2 models

> hide #!3.2 models

> show #!3.3 models

> hide #!3.3 models

> show #!3.2 models

> hide #!3.2 models

> show #!3.3 models

> hide #!3.3 models

> show #!3.4 models

> hide #!3.4 models

> show #!3.5 models

> hide #!3.5 models

> hide #!3.1 models

> hide #!1.2 models

> show #!3.1 models

> hide #!3.1.2 models

> show #!3.1.2 models

> hide #!3.1.1 models

> show #!3.1.1 models

> select #3.1.2/A:140

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

> show sel atoms

> style sel stick

Changed 8 atom styles  

> select #1.1.2/A:816

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

> show sel atoms

> select #3.1.2/A:137

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

> show sel atoms

> style sel stick

Changed 11 atom styles  

> select #1.1.2/A:812

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

> show sel atoms

> save ""/Users/zang/Postdoc/Ablasser/TIR/STING-TIR
> chimera/SfSTING(7UN8)_SARM1TIR(7NAK)_TLR4TIR_structures_2025-10-31-15-56-8/SfSTING(7UN8)_TLR4TIR_SARM1TIR(7NAK).cxs""

> select #1.1.2/A:795

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

> select #3.1.2/A:115

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

> show sel atoms

> style sel stick

Changed 7 atom styles  

> select #1.1.2/A:793

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

> show sel atoms

> save ""/Users/zang/Postdoc/Ablasser/TIR/STING-TIR
> chimera/SfSTING(7UN8)_SARM1TIR(7NAK)_TLR4TIR_structures_2025-10-31-15-56-8/SfSTING(7UN8)_TLR4TIR_SARM1TIR(7NAK).cxs""

> select #1.1.2/A:806

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

> show sel atoms

> style sel stick

Changed 8 atom styles  

> select #3.1.2/A:132

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

> show sel atoms

> style sel stick

Changed 8 atom styles  

> save ""/Users/zang/Postdoc/Ablasser/TIR/STING-TIR
> chimera/SfSTING(7UN8)_SARM1TIR(7NAK)_TLR4TIR_structures_2025-10-31-15-56-8/SfSTING(7UN8)_TLR4TIR_SARM1TIR(7NAK).cxs""

> select #1.1.2/A:677

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

> show sel atoms

> select #3.1.2/A:6

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

> show sel atoms

> style sel stick

Changed 11 atom styles  

> save ""/Users/zang/Postdoc/Ablasser/TIR/STING-TIR
> chimera/SfSTING(7UN8)_SARM1TIR(7NAK)_TLR4TIR_structures_2025-10-31-15-56-8/SfSTING(7UN8)_TLR4TIR_SARM1TIR(7NAK).cxs""

Unsupported scale factor (0.000000) detected on Display1  

[Repeated 8 time(s)]

> save ""/Users/zang/Postdoc/Ablasser/TIR/STING-TIR
> chimera/SfSTING(7UN8)_SARM1TIR(7NAK)_TLR4TIR_structures_2025-10-31-15-56-8/SfSTING(7UN8)_TLR4TIR_SARM1TIR(7NAK).cxs""

> close session

> open ""/Users/zang/Postdoc/Ablasser/TIR/STING-TIR
> chimera/SfSTING(7UN8)_SARM1TIR(7NAK)_TLR5TIR(3J0A)/3J0A.A.cif""

Summary of feedback from opening /Users/zang/Postdoc/Ablasser/TIR/STING-TIR
chimera/SfSTING(7UN8)_SARM1TIR(7NAK)_TLR5TIR(3J0A)/3J0A.A.cif  
---  
notes | PDBx/mmCIF styling lost on line 5095. Rereading mmCIF file from the beginning.  
Fetching CCD FUC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/FUC/FUC.cif  
Fetching CCD NAG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NAG/NAG.cif  
  
3J0A.A.cif title:  
Homology model of human Toll-like receptor 5 fitted into an electron
microscopy single particle reconstruction [more info...]  
  
Chain information for 3J0A.A.cif #1  
---  
Chain | Description | UniProt  
A B | Toll-like receptor 5 | TLR5_HUMAN 23-858  
  
Non-standard residues in 3J0A.A.cif #1  
---  
FUC — alpha-L-fucopyranose (alpha-L-fucose;6-deoxy-alpha-L-
galactopyranose;L-fucose;fucose)  
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)  
  

> open ""/Users/zang/Postdoc/Ablasser/TIR/STING-TIR
> chimera/SfSTING(7UN8)_SARM1TIR(7NAK)_TLR5TIR(3J0A)/7NAK.A.cif""

Summary of feedback from opening /Users/zang/Postdoc/Ablasser/TIR/STING-TIR
chimera/SfSTING(7UN8)_SARM1TIR(7NAK)_TLR5TIR(3J0A)/7NAK.A.cif  
---  
note | PDBx/mmCIF styling lost on line 12768. Rereading mmCIF file from the beginning.  
  
7NAK.A.cif title:  
Cryo-EM structure of activated human SARM1 in complex with NMN and 1AD
(TIR:1AD) [more info...]  
  
Chain information for 7NAK.A.cif #2  
---  
Chain | Description | UniProt  
A B C D E F G H | NAD(+) hydrolase SARM1 | SARM1_HUMAN 28-724  
  
Non-standard residues in 7NAK.A.cif #2  
---  
1QD —
[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-
oxidanyl-phosphoryl]
[(2~{R},3~{S},4~{R},5~{R})-5-(5-iodanylisoquinolin-2-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl
hydrogen phosphate  
  

> open ""/Users/zang/Postdoc/Ablasser/TIR/STING-TIR
> chimera/SfSTING(7UN8)_SARM1TIR(7NAK)_TLR5TIR(3J0A)/7UN8.A.cif""

Summary of feedback from opening /Users/zang/Postdoc/Ablasser/TIR/STING-TIR
chimera/SfSTING(7UN8)_SARM1TIR(7NAK)_TLR5TIR(3J0A)/7UN8.A.cif  
---  
note | PDBx/mmCIF styling lost on line 4604. Rereading mmCIF file from the beginning.  
  
7UN8.A.cif title:  
SfSTING with c-di-GMP single fiber [more info...]  
  
Chain information for 7UN8.A.cif #3  
---  
Chain | Description | UniProt  
A B C D E F | CD-NTase-associated protein 12 | CAP12_SPHFK 2-323  
  
Non-standard residues in 7UN8.A.cif #3  
---  
C2E —
9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)
(c-di-GMP;Cyclic diguanosine monophosphate)  
  

> hide atoms

> show cartoons

> select :1QD

432 atoms, 472 bonds, 8 residues, 1 model selected  

> show sel atoms

> select #2/1qD

Nothing selected  

> select #2/1QD

Nothing selected  

> select #3/A:2-322

2324 atoms, 2360 bonds, 3 pseudobonds, 297 residues, 2 models selected  

> select :1QD

432 atoms, 472 bonds, 8 residues, 1 model selected  

> show target m

> split #2

Split 7NAK.A.cif (#2) into 8 models  
Chain information for 7NAK.A.cif A #2.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 7NAK.A.cif B #2.2  
---  
Chain | Description  
B | No description available  
  
Chain information for 7NAK.A.cif C #2.3  
---  
Chain | Description  
C | No description available  
  
Chain information for 7NAK.A.cif D #2.4  
---  
Chain | Description  
D | No description available  
  
Chain information for 7NAK.A.cif E #2.5  
---  
Chain | Description  
E | No description available  
  
Chain information for 7NAK.A.cif F #2.6  
---  
Chain | Description  
F | No description available  
  
Chain information for 7NAK.A.cif G #2.7  
---  
Chain | Description  
G | No description available  
  
Chain information for 7NAK.A.cif H #2.8  
---  
Chain | Description  
H | No description available  
  

> split #3

Split 7UN8.A.cif (#3) into 6 models  
Chain information for 7UN8.A.cif A #3.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 7UN8.A.cif B #3.2  
---  
Chain | Description  
B | No description available  
  
Chain information for 7UN8.A.cif C #3.3  
---  
Chain | Description  
C | No description available  
  
Chain information for 7UN8.A.cif D #3.4  
---  
Chain | Description  
D | No description available  
  
Chain information for 7UN8.A.cif E #3.5  
---  
Chain | Description  
E | No description available  
  
Chain information for 7UN8.A.cif F #3.6  
---  
Chain | Description  
F | No description available  
  

> hide #2.1 models

> show #2.1 models

> hide #2.1 models

> hide #2.2 models

> hide #2.3 models

> hide #2.5 models

> hide #2.6 models

> hide #2.7 models

> split #1

Split 3J0A.A.cif (#1) into 16 models  
Chain information for 3J0A.A.cif A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 3J0A.A.cif B #1.2  
---  
Chain | Description  
B | No description available  
  

> hide #!1.1 models

> show #!1.1 models

> hide #!1.2 models

> hide #1.3 models

> show #1.3 models

> hide #1.3 models

> hide #1.16 models

> hide #1.15 models

> hide #1.14 models

> hide #1.13 models

> hide #1.12 models

> hide #1.11 models

> hide #1.10 models

> hide #1.9 models

> hide #1.8 models

> hide #1.7 models

> hide #1.6 models

> hide #1.5 models

> hide #1.4 models

> show #1.3 models

> hide #1.3 models

> show #!1.2 models

> show #1.3 models

> hide #!1.2 models

> show #1.4 models

> hide #!1.1 models

> show #!1.1 models

> select #1/A

6437 atoms, 6591 bonds, 2 pseudobonds, 797 residues, 2 models selected  

> select #1.1/A:23-845

6437 atoms, 6591 bonds, 2 pseudobonds, 797 residues, 2 models selected  

> select #1/A ATOMS : 681-845

Expected a keyword  

> select #1/A atoms : 681-845

Expected a keyword  

> select #1/A atoms: 681-845

Expected a keyword  

> select #1/A atoms: 681 - 845

Expected a keyword  

> select #1/A atoms : 681 - 845

Expected a keyword  

> split #1/A atoms : 681 \- 845

Expected a keyword  

> split #1/A atoms : 681-845

Split 3J0A.A.cif A (#1.1) into 2 models  
Chain information for 3J0A.A.cif A 1 #1.1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 3J0A.A.cif A 2 #1.1.2  
---  
Chain | Description  
A | No description available  
  

> hide #1.1.1 models

> show #1.1.1 models

> hide #!1.1.2 models

> save ""/Users/zang/Postdoc/Ablasser/TIR/STING-TIR
> chimera/SfSTING(7UN8)_SARM1TIR(7NAK)_TLR5TIR(3J0A)/SfSTING(7UN8)_TLR5TIR(3J0A)_SARM1TIR(7NAK).cxs""

——— End of log from Sun Nov 2 15:17:32 2025 ———

> view name session-start

opened ChimeraX session  

> hide #!3.2 models

> hide #!3.3 models

> hide #!3.4 models

> hide #!3.5 models

> hide #!3.6 models

> hide #2.8 models

> select add #3.1

2324 atoms, 2360 bonds, 3 pseudobonds, 297 residues, 2 models selected  

> select subtract #3.1

Nothing selected  

> select add #2.4

2297 atoms, 2328 bonds, 141 residues, 1 model selected  

> color sel light gray

> color sel hot pink

> color sel dim gray

> color sel magenta

> color sel orange

> color sel orange red

> select clear

> select add #2.4

2297 atoms, 2328 bonds, 141 residues, 1 model selected  

> select subtract #2.4

Nothing selected  

> select add #3.1

2324 atoms, 2360 bonds, 3 pseudobonds, 297 residues, 2 models selected  

> select subtract #3.1

Nothing selected  

> select add #2.4

2297 atoms, 2328 bonds, 141 residues, 1 model selected  

> select subtract #2.4

Nothing selected  

> select add #1

11828 atoms, 12115 bonds, 2 pseudobonds, 1457 residues, 21 models selected  

> select subtract #1

Nothing selected  

> hide #2.4 models

> show #2.4 models

> hide #!3.1 models

> show #2.5 models

> hide #2.5 models

> show #2.3 models

> select add #3.1

2324 atoms, 2360 bonds, 3 pseudobonds, 297 residues, 2 models selected  

> select subtract #3.1

Nothing selected  

> show #!3.1 models

> hide #!1 models

> show #!1 models

> hide #!3.1 models

> show #!3.1 models

> hide #2.3 models

> hide #2.4 models

> select #3.1/A:9

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

> show sel atoms

> style sel stick

Changed 6 atom styles  

> select #1.1.1/A:699

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

> select clear

> select #3.1/A:9

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

> show sel atoms

> hide sel atoms

> select clear

> select #3.1/A:10

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

> show sel atoms

> style sel stick

Changed 6 atom styles  

> select #1.1.1/A:700

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

> show sel atoms

> select #3.1/A:142

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

> show sel atoms

> style sel stick

Changed 9 atom styles  

> select #1.1.1/A:839

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

> show sel atoms

> select #1.1.1/A:838

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

> show sel atoms

> select #1.1.1/A:839

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

> hide sel atoms

> save ""/Users/zang/Postdoc/Ablasser/TIR/STING-TIR
> chimera/SfSTING(7UN8)_SARM1TIR(7NAK)_TLR5TIR(3J0A)/SfSTING(7UN8)_TLR5TIR(3J0A)_SARM1TIR(7NAK).cxs""

> open ""/Users/zang/Postdoc/Ablasser/TIR/STING-TIR chimera/Structure-based AA
> alignment_SfSTING, TLR4, TLR5, SARM1.aln""

Summary of feedback from opening /Users/zang/Postdoc/Ablasser/TIR/STING-TIR
chimera/Structure-based AA alignment_SfSTING, TLR4, TLR5, SARM1.aln  
---  
notes | Alignment identifier is Structure-based AA alignment_SfSTING, TLR4, TLR5, SARM1.aln  
Associated 7NAK.A.cif A (2.1) chain A to 7NAK.A with 0 mismatches  
Associated 7NAK.A.cif B (2.2) chain B to 7NAK.A with 0 mismatches  
Associated 7NAK.A.cif C (2.3) chain C to 7NAK.A with 0 mismatches  
Associated 7NAK.A.cif D (2.4) chain D to 7NAK.A with 0 mismatches  
Associated 7NAK.A.cif E (2.5) chain E to 7NAK.A with 0 mismatches  
3 messages similar to the above omitted  
Associated 7UN8.A.cif A (3.1) chain A to 7UN8.A with 0 mismatches  
Associated 7UN8.A.cif B (3.2) chain B to 7UN8.A with 0 mismatches  
Associated 7UN8.A.cif D (3.4) chain D to 7UN8.A with 0 mismatches  
Associated 7UN8.A.cif F (3.6) chain F to 7UN8.A with 0 mismatches  
Associated 3J0A.A.cif A 1 (1.1.1) chain A to 3J0A.A with 0 mismatches  
Showing conservation header (""seq_conservation"" residue attribute) for
alignment Structure-based AA alignment_SfSTING, TLR4, TLR5, SARM1.aln  
  
Opened 6 sequences from Structure-based AA alignment_SfSTING, TLR4, TLR5,
SARM1.aln  

> close session

> open ""/Users/zang/Postdoc/Ablasser/TIR/STING-TIR chimera/Structure-based AA
> alignment_SfSTING, TLR4, TLR5, SARM1.aln"" format aln

Summary of feedback from opening /Users/zang/Postdoc/Ablasser/TIR/STING-TIR
chimera/Structure-based AA alignment_SfSTING, TLR4, TLR5, SARM1.aln  
---  
notes | Alignment identifier is Structure-based AA alignment_SfSTING, TLR4, TLR5, SARM1.aln  
Showing conservation header (""seq_conservation"" residue attribute) for
alignment Structure-based AA alignment_SfSTING, TLR4, TLR5, SARM1.aln  
  
Opened 6 sequences from Structure-based AA alignment_SfSTING, TLR4, TLR5,
SARM1.aln  

> open ""/Users/zang/Postdoc/Ablasser/TIR/STING-TIR
> chimera/SfSTING(7UN8)_SARM1TIR(7NAK)_TLR4TIR_structures_2025-10-31-15-56-8/SfSTING(7UN8)_TLR4TIR_SARM1TIR(7NAK).cxs""
> format session

> view name session-start

opened ChimeraX session  

> close session

> open ""/Users/zang/Postdoc/Ablasser/TIR/STING-TIR
> chimera/SfSTING(7UN8)_SARM1TIR(7NAK)_TLR5TIR(3J0A)/SfSTING(7UN8)_TLR5TIR(3J0A)_SARM1TIR(7NAK).cxs""
> format session

> view name session-start

opened ChimeraX session  

> split #3.1 atoms : 145-322

Split 7UN8.A.cif A (#3.1) into 2 models  
Chain information for 7UN8.A.cif A 1 #3.1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 7UN8.A.cif A 2 #3.1.2  
---  
Chain | Description  
A | No description available  
  

> hide #!3.1.2 models

> show #!3.1.2 models

> hide #!3.1.1 models

> select clear

> graphics silhouettes true

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting flat

> lighting full

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> set bgColor white

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting flat

> lighting full

> lighting soft

> lighting simple

> graphics silhouettes false

> graphics silhouettes true

> lighting simple

> lighting soft

> lighting simple

> lighting full

> nucleotides #1.3-4#1.1.1#!3.1.2 atoms

> style nucleic & #1.3-4#1.1.1#!3.1.2 stick

Changed 0 atom styles  

> nucleotides #1.3-4#1.1.1#!3.1.2 tube/slab shape box

> select helix

17266 atoms, 17366 bonds, 1562 residues, 18 models selected  

> select clear

> cartoon style #1.3-4#1.1.1#3.1.2#!1-3#!1.1#!3.1 modeHelix tube sides 20

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting full

> lighting soft

> lighting simple

> lighting full

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting full

> lighting soft

> lighting simple

Drag select of 11 residues  

> hide sel cartoons

> hide #!1 models

> show #!1 models

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true intensity 0.5

> lighting full

> lighting flat

> lighting soft

> lighting simple

> graphics silhouettes false

> graphics silhouettes true

> lighting soft

> set bgColor black

> set bgColor gray

> set bgColor white

> lighting full

> lighting simple

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting full

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting simple

> view

> save /Users/zang/Desktop/image1.png supersample 3

> select add #3.1.2

1070 atoms, 1012 bonds, 2 pseudobonds, 138 residues, 3 models selected  

> color (#1.1.1#!3.1.2 & sel) magenta

> undo

> color (#1.1.1#!3.1.2 & sel) forest green

> undo

> color (#1.1.1#!3.1.2 & sel) light sea green

> undo

> color (#1.1.1#!3.1.2 & sel) medium blue

> undo

> ui tool show ""Color Actions""

> color sel medium spring green

> color sel medium aquamarine

> color sel salmon

> color sel light salmon

> color sel spring green

> color sel cyan

> color sel medium spring green

> color sel light salmon

> color sel sandy brown

> color sel spring green

> color sel lawn green

> color sel lime green

> color sel medium aquamarine

> color sel teal

> color sel steel blue

> color sel cadet blue

> color sel light slate gray

> color sel yellow

> color sel light salmon

> select subtract #3.1.2

69 atoms, 9 residues, 1 model selected  

> select add #1

11828 atoms, 12115 bonds, 2 pseudobonds, 1457 residues, 21 models selected  

> select subtract #1

Nothing selected  

> select add #3.1

2324 atoms, 2359 bonds, 3 pseudobonds, 297 residues, 5 models selected  

> color sel navajo white

> color sel antique white

> color sel wheat

> color sel alice blue

> color sel khaki

> color sel pale goldenrod

> color sel lemon chiffon

> color sel light yellow

> color sel seashell

> color sel cornsilk

> color sel lavender blush

> color sel papaya whip

> color sel blanched almond

> color sel moccasin

> color sel navajo white

> color sel peach puff

> color sel pink

> color sel old lace

> color sel light goldenrod yellow

> color sel linen

> color sel ivory

> color sel light yellow

> color sel gainsboro

> color sel lavender

> color sel khaki

> color sel alice blue

> color sel wheat

> color sel navajo white

> color sel blanched almond

> color sel light green

> color sel pale green

> color sel tan

> color sel lavender

> color sel light gray

> color sel gray

> color sel light gray

> color sel silver

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> lighting simple

> lighting soft

> lighting full

> lighting flat

> lighting simple

> color sel aquamarine

> color sel sky blue

> color sel light sky blue

> color sel light blue

> color sel light sky blue

> select clear


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

Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 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 M4 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: Mac16,8
      Model Number: Z1FE0012KSM/A
      Chip: Apple M4 Pro
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 48 GB
      System Firmware Version: 13822.1.2
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.7.1 (24G231)
      Kernel Version: Darwin 24.6.0
      Time since boot: 1 day, 36 minutes

Graphics/Displays:

    Apple M4 Pro:

      Chipset Model: Apple M4 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      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: No
          Connection Type: Internal
        DELL P2719H:
          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
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.6.1
    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: 14.1.19
    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: 1.10.1
    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: 1.1.3
    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: 7.10.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.15
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.59.0
    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: 4.3.2
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    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: 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
    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
    Pygments: 2.18.0
    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
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.1
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14
}}}
"	defect	closed	normal		Platform		duplicate						all	ChimeraX