![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 weeks ago
Closed 4 weeks ago
#19287 closed defect (duplicate)
mshMIGPerform crash in NSAccessiblity native Mac APIs
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Platform | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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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{
"uptime" : 22000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac16,8",
"coalitionID" : 2642,
"osVersion" : {
"train" : "macOS 15.7.1",
"build" : "24G231",
"releaseType" : "User"
},
"captureTime" : "2025-11-04 09:41:54.3528 +0100",
"codeSigningMonitor" : 2,
"incident" : "11CF67E0-EB26-4AA7-9875-A76798CFE3E7",
"pid" : 12123,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-11-03 15:11:46.1670 +0100",
"procStartAbsTime" : 118923158213,
"procExitAbsTime" : 537070081637,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.10.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.1","CFBundleVersion":"1.10.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"361D5FA6-5171-5CF6-9643-AA01D85B6C3A","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "A9778062-33A8-9A3E-FF6E-B4E28960D362",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["notOptedIn","siriAssetIsNotReady","assetIsNotReady"]},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
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"bootSessionUUID" : "CBA00B66-0436-4CA1-81E0-507FBD70D430",
"wakeTime" : 3693,
"sleepWakeUUID" : "2B05FAE0-7F40-438B-907B-36CCC24C5D07",
"sip" : "enabled",
"exception" : {"codes":"0x0000000000000001, 0x000000019e120dac","rawCodes":[1,6946950572],"type":"EXC_BREAKPOINT","signal":"SIGTRAP"},
"termination" : {"flags":0,"code":5,"namespace":"SIGNAL","indicator":"Trace\/BPT trap: 5","byProc":"exc handler","byPid":12123},
"os_fault" : {"process":"ChimeraX"},
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===== 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
Change History (2)
comment:1 by , 4 weeks ago
| Component: | Unassigned → Platform |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → mshMIGPerform crash in NSAccessiblity native Mac APIs |
comment:2 by , 4 weeks ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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