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Opened 3 hours ago
#19504 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-26.1-arm64-arm-64bit
ChimeraX Version: 1.11rc202512030952 (2025-12-03 09:52:55 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000001fafce080 (most recent call first):
File "/Applications/ChimeraX-1.11-rc2025.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 414 in event_loop
File "/Applications/ChimeraX-1.11-rc2025.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1064 in init
File "/Applications/ChimeraX-1.11-rc2025.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb_lib._load_libs, PIL._imaging, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, PIL._imagingmath, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, kiwisolver._cext, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 54)
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"procLaunch" : "2025-12-09 15:03:24.5677 +0100",
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"wakeTime" : 2116,
"sleepWakeUUID" : "C09A0B02-101C-4FEF-A3F7-D29979150EBF",
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"vmRegionInfo" : "0x8 is not in any region. Bytes before following region: 4370726904
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 104840000-104844000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.11-rc2025.12.03.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000008","rawCodes":[1,8],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000008"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":87010},
"vmregioninfo" : "0x8 is not in any region. Bytes before following region: 4370726904
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
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--->
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===== Log before crash start =====
UCSF ChimeraX version: 1.11rc202512030952 (2025-12-03)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/jxq794/Desktop/gcgr_comparison/temp/gcgr_nnc-9204-1702_model.cif
Chain information for gcgr_nnc-9204-1702_model.cif #1
---
Chain | Description
A | .
R | .
Computing secondary structure
> open 5YQZ fromDatabase pdb format mmcif
Summary of feedback from opening 5YQZ fetched from pdb
---
note | Fetching compressed mmCIF 5yqz from http://files.rcsb.org/download/5yqz.cif
5yqz title:
Structure of the glucagon receptor in complex with a glucagon analogue [more
info...]
Chain information for 5yqz #2
---
Chain | Description | UniProt
P | Glucagon analogue |
R | Glucagon receptor,Endolysin,Glucagon receptor | GLR_HUMAN 27-257 260-432, D9IEF7_BPT4 1001-1160
Non-standard residues in 5yqz #2
---
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)
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)
PO4 — phosphate ion
> ui tool show Matchmaker
> matchmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5yqz, chain R (#2) with gcgr_nnc-9204-1702_model.cif, chain A (#1),
sequence alignment score = 1930.9
RMSD between 262 pruned atom pairs is 1.213 angstroms; (across all 400 pairs:
4.937)
> open 8YW5 fromDatabase pdb format mmcif
8yw5 title:
Cryo-EM structure of the retatrutide-bound human GCGR-Gs complex [more
info...]
Chain information for 8yw5 #3
---
Chain | Description | UniProt
A | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | GNAS2_HUMAN 1-394
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340
G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71
N | Nanobody-35 |
P | Retatrutide |
R | Glucagon receptor | GLR_HUMAN 27-432
> hide #2 models
> show #2 models
> hide #1 models
> hide #2 models
> open /Users/jxq794/Desktop/gcgr_comparison/temp/gcgr_retatrutide_model.cif
Chain information for gcgr_retatrutide_model.cif #4
---
Chain | Description
A | .
R | .
Computing secondary structure
> show #4#!3 cartoons
> hide #4#!3 atoms
> ui tool show Matchmaker
> matchmaker #4 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8yw5, chain R (#3) with gcgr_retatrutide_model.cif, chain A (#4),
sequence alignment score = 1977.9
RMSD between 314 pruned atom pairs is 0.908 angstroms; (across all 379 pairs:
1.758)
> ui tool show "Show Sequence Viewer"
> sequence chain #4/R
Alignment identifier is 4/R
> hide #!3 models
> rainbow #4
> color #4 bychain
> hide #4 models
> show #!3 models
> hide #!3 models
> show #2 models
> view
> lighting shadows true
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> color #2 bychain
> show #1 models
> hide #2 models
> show #!3 models
> hide #1 models
> show #4 models
> show #1 models
> hide #1 models
> ui tool show Matchmaker
> matchmaker #4 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8yw5, chain R (#3) with gcgr_retatrutide_model.cif, chain A (#4),
sequence alignment score = 1977.9
RMSD between 314 pruned atom pairs is 0.908 angstroms; (across all 379 pairs:
1.758)
> view
> show #1 models
> hide #1 models
Color zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic
models, 0 maps.
> ui tool show Matchmaker
> matchmaker #1,4#!3 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5yqz, chain R (#2) with gcgr_nnc-9204-1702_model.cif, chain A (#1),
sequence alignment score = 1930.9
RMSD between 262 pruned atom pairs is 1.213 angstroms; (across all 400 pairs:
4.937)
Matchmaker 5yqz, chain R (#2) with gcgr_retatrutide_model.cif, chain A (#4),
sequence alignment score = 1929.7
RMSD between 251 pruned atom pairs is 1.260 angstroms; (across all 400 pairs:
4.982)
Matchmaker 5yqz, chain R (#2) with 8yw5, chain R (#3), sequence alignment
score = 1810.9
RMSD between 217 pruned atom pairs is 1.134 angstroms; (across all 379 pairs:
5.207)
> view
> show #2 models
> show #1 models
> hide #1 models
> hide #2 models
> hide #4 models
> interfaces #!3 & ~solvent
6 buried areas: B G 2005, R P 1734, B A 1345, R A 1340, A N 821, B N 460
> color sel byhetero
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel stick
Changed 302 atom styles
> color sel red
> color sel byhetero
> show #4 models
> hide #!3 models
> interfaces #4 & ~solvent
1 buried areas: A R 2102
> show sel atoms
> color sel orange red
> color sel byhetero
> show #!3 models
> color sel yellow
> ui tool show "Color Actions"
> color sel #fffffffe
> color sel #fffffff9
> color sel #fffffff1
> color sel #fffffff0
> color sel #ffffffef
> color sel #ffffffed
> color sel #ffffffe9
> color sel #ffffffe7
> color sel #ffffffe5
> color sel #ffffffe2
> color sel #ffffffde
> color sel #ffffffdd
> color sel #ffffffdb
> color sel #ffffffd8
> color sel #ffffffd6
> color sel #ffffffd3
> color sel #ffffffd0
> color sel #ffffffce
> color sel #ffffffcb
> color sel #ffffffc8
> color sel #ffffffc6
> color sel #ffffffc5
> color sel #ffffffc3
> color sel #ffffffc2
> color sel #ffffffc1
> color sel #ffffffc2
> color sel #ffffffc3
> color sel #ffffffc5
> color sel #ffffffc6
> color sel #ffffffc9
> color sel #ffffffcc
> color sel #ffffffcd
> color sel #ffffffce
> color sel #ffffffcf
> color sel #ffffffd0
> color sel #ffffffd1
> color sel #ffffffd2
> color sel #ffffffd3
> color sel #ffffffd4
> color sel #ffffffd5
> color sel #ffffffd6
> color sel #ffffffd7
> color sel #ffffffd8
> color sel #ffffffd9
> color sel #ffffffda
> color sel #ffffffdb
> color sel #ffffffdc
> color sel #ffffffdd
> color sel #ffffffde
> color sel #ffffffdf
> color sel #ffffffe0
> color sel #ffffffe1
> color sel #ffffffe2
> color sel #ffffffe3
> color sel #ffffffe4
> color sel #ffffffe5
> color sel #ffffffe6
> color sel #ffffffe7
> color sel #ffffffe8
> color sel #ffffffe9
> color sel #ffffffea
> color sel #ffffffeb
> color sel #ffffffec
> color sel #ffffffed
> color sel #ffffffee
> color sel #fffffff0
> color sel #fffffff1
> color sel #fffffff2
> color sel #fffffff3
> color sel #fffffff4
> color sel #fffffff5
> color sel #fffffff6
> color sel #fffffff7
> color sel #fffffff8
> color sel #fffffff9
> color sel #fffffff8
> color sel #fffffff9
> color sel #fffffffa
> color sel #fffffffb
> color sel #fffffffc
> color sel #fffffffd
> color sel #fffffffe
> color sel #ffffffff
> color sel #fffffff5
> color sel #fffffff3
> color sel #fffffff2
> color sel #fffffff3
> color sel #fffffff4
> color sel #fffffff5
> color sel #fffffff6
> color sel #fffffff7
> color sel #fffffff8
> color sel #fffffff9
> color sel #fffffffa
> color sel #fffffffb
> color sel #fffffffc
> color sel #fffffffd
> color sel #ffffffff
> color sel #fffffff6
> color sel #ffffffeb
> color sel #ffffffdd
> color sel #ffffffbe
> color sel #ffffffac
> color sel #ffffffa6
> color sel #ffffff93
> color sel #ffffff8d
> color sel #ffffff89
> color sel #ffffff81
> color sel #ffffff80
> color sel #ffffff76
> color sel #ffffff75
> color sel #ffffff74
> color sel #ffffff71
> color sel #ffffff6a
> color sel #ffffff66
> color sel #ffffff63
> color sel #ffffff5f
> color sel #ffffff5b
> color sel #ffffff58
> color sel #ffffff56
> color sel #ffffff55
> color sel #ffffff53
> color sel #ffffff52
> color sel #ffffff51
> color sel #ffffff50
> color sel #ffffff4d
> color sel #ffffff4b
> color sel #ffffff49
> color sel #ffffff48
> color sel #ffffff46
> color sel #ffffff45
> color sel #ffffff43
> color sel #ffffff42
> color sel #ffffff41
> color sel #ffffff40
> color sel #ffffff3f
> color sel #ffffff40
> color sel #ffffff41
> color sel #ffffff42
> color sel #ffffff44
> color sel #ffffff45
> color sel #ffffff46
> color sel #ffffff48
> color sel #ffffff4b
> color sel #ffffff4d
> color sel #ffffff4f
> color sel #ffffff51
> color sel #ffffff53
> color sel #ffffff54
> color sel #ffffff56
> color sel #ffffff59
> color sel #ffffff5a
> color sel #ffffff5c
> color sel #ffffff62
> color sel #ffffff64
> color sel #ffffff67
> color sel #ffffff6a
> color sel #ffffff6c
> color sel #ffffff6f
> color sel #ffffff71
> color sel #ffffff73
> color sel #ffffff75
> color sel #ffffff76
> color sel #ffffff77
> color sel #ffffff78
> color sel #ffffff79
> color sel #ffffff7a
> color sel #ffffff7b
> color sel #ffffff7c
> color sel #ffffff7d
> color sel #ffffff7e
> color sel #ffffff7f
> color sel #ffffff80
> color sel #ffffff89
> color sel #ffffff8b
> color sel #ffffff8c
> color sel #ffffff8e
> color sel #ffffff8f
> color sel #ffffff91
> color sel #ffffff93
> color sel #ffffff95
> color sel #ffffff97
> color sel #ffffff9a
> color sel #ffffff9c
> color sel #ffffff9f
> color sel #ffffffa1
> color sel #ffffffa3
> color sel #ffffffa4
> color sel #ffffffa5
> color sel #ffffffa6
> color sel #ffffffa7
> color sel #ffffffa8
> color sel #ffffffa7
> color sel #ffffffa5
> color sel #ffffffa4
> color sel #ffffffa2
> color sel #ffffffa1
> color sel #ffffff9f
> color sel #ffffff9e
> color sel #ffffff9d
> color sel #ffffff9c
> color sel #ffffff9b
> color sel #ffffff9a
> color sel #ffffff99
> color sel #ffffff97
> color sel #ffffff96
> color sel #ffffff95
> color sel #ffffff94
> color sel #ffffff93
> color sel #ffffff92
> color sel #ffffff91
> color sel #ffffff90
> color sel #ffffff8f
> color sel #ffffff8e
> color sel #ffffff8d
> color sel #fbff908d
> color sel #fcff908d
> color sel #feff908d
> color sel #feff8f8d
> color sel #feff8e8d
> color sel #fdff8d8d
> color sel #fdff8b8d
> color sel #fcff898d
> color sel #fcff858d
> color sel #fcff828d
> color sel #fcff808d
> color sel #fcff7e8d
> color sel #fcff7d8d
> color sel #fcff7b8d
> color sel #fcff7a8d
> color sel #fcff798d
> color sel #fbff788d
> color sel #fbff778d
> color sel #faff768d
> color sel #faff758d
> color sel #faff748d
> color sel #faff738d
> color sel #faff728d
> color sel #faff718d
> color sel #faff6e8d
> color sel #fbff6a8d
> color sel #fcff658d
> color sel #feff608d
> color sel #ffff5b8d
> color sel #fffe568d
> color sel #fffd528d
> color sel #fffc4f8d
> color sel #fffb4d8d
> color sel #fffb4c8d
> color sel #fffa4b8d
> color sel #fffa4a8d
> color sel #fffa498d
> color sel #fffb498d
> color sel #fffb488d
> color sel #fffb478d
> color sel #fffb468d
> color sel #fffb458d
> color sel #fffb448d
> color sel #fffb438d
> color sel #fffb428d
> color sel #fffb408d
> color sel #fffb3f8d
> color sel #fffa3e8d
> color sel #fffb3f8d
> color sel #fffb3f81
> color sel #fffb3f82
> color sel #fffb3f83
> color sel #fffb3f84
> color sel #fffb3f85
> color sel #fffb3f86
> color sel #fffb3f87
> color sel #fffb3f88
> color sel #fffb3f89
> color sel #fffb3f8a
> color sel #fffb3f8b
> color sel #fffb3f8c
> color sel #fffb3f8d
> color sel #fffb3f91
> color sel #fffb3f93
> color sel #fffb3f95
> color sel #fffb3f98
> color sel #fffb3f9b
> color sel #fffb3f9f
> color sel #fffb3fa2
> color sel #fffb3fa3
> color sel #fffb3fa4
> color sel #fffb3fa5
> color sel #fffb3fa6
> color sel #fffb3fa7
> color sel #fffb3fa8
> color sel #fffb3fa9
> color sel #fffb3faa
> color sel #fffb3fab
> color sel #fffb3fac
> color sel #fffb3fae
> color sel #fffb3fb1
> color sel #fffb3fb4
> color sel #fffb3fb5
> color sel #fffb3fb6
> color sel #fffb3fb7
> color sel #fffb3fb8
> color sel #fffb3fb9
> color sel #fffb3fba
> color sel #fffb3fbb
> color sel #fffb3fbc
> color sel #fffb3fbd
> color sel #fffb3fc0
> color sel #fffb3fc2
> color sel #fffb3fc4
> color sel #fffb3fc5
> color sel #fffb3fc7
> color sel #fffb3fc8
> color sel #fffb3fc9
> color sel #fffb3fca
> hide #!3 models
> show #!3 models
> show #2 models
> hide #2 models
> close #2
> close #3
> open /Users/jxq794/Desktop/gcgr_comparison/temp/gcgr_adomeglivant_model.cif
Summary of feedback from opening
/Users/jxq794/Desktop/gcgr_comparison/temp/gcgr_adomeglivant_model.cif
---
warning | Unable to fetch template for 'LIG_R': will connect using distance criteria
Chain information for gcgr_adomeglivant_model.cif #2
---
Chain | Description
A | .
> open /Users/jxq794/Desktop/gcgr_comparison/temp/gcgr_nnc-9204-1702_model.cif
Chain information for gcgr_nnc-9204-1702_model.cif #3
---
Chain | Description
A | .
R | .
> open /Users/jxq794/Desktop/gcgr_comparison/temp/gcgr_glucagon_model.cif
Chain information for gcgr_glucagon_model.cif #5
---
Chain | Description
A | .
R | .
> open /Users/jxq794/Desktop/gcgr_comparison/temp/gcgr_nnc-9204-0043_model.cif
Chain information for gcgr_nnc-9204-0043_model.cif #6
---
Chain | Description
A | .
R | .
> open /Users/jxq794/Desktop/gcgr_comparison/temp/gcgr_cotadutide_model.cif
Chain information for gcgr_cotadutide_model.cif #7
---
Chain | Description
A | .
R | .
> open /Users/jxq794/Desktop/gcgr_comparison/temp/gcgr_survodutide_model.cif
Chain information for gcgr_survodutide_model.cif #8
---
Chain | Description
A | .
R | .
> open /Users/jxq794/Desktop/gcgr_comparison/temp/gcgr_retatrutide_model.cif
Chain information for gcgr_retatrutide_model.cif #9
---
Chain | Description
A | .
R | .
Computing secondary structure
> close #3
> show #1 models
> ui tool show Matchmaker
> matchmaker #1-2,4,6-9 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker gcgr_glucagon_model.cif, chain A (#5) with
gcgr_nnc-9204-1702_model.cif, chain A (#1), sequence alignment score = 2337.2
RMSD between 416 pruned atom pairs is 0.394 angstroms; (across all 435 pairs:
0.942)
Matchmaker gcgr_glucagon_model.cif, chain A (#5) with
gcgr_adomeglivant_model.cif, chain A (#2), sequence alignment score = 2310.2
RMSD between 373 pruned atom pairs is 0.806 angstroms; (across all 435 pairs:
10.796)
Matchmaker gcgr_glucagon_model.cif, chain A (#5) with
gcgr_retatrutide_model.cif, chain A (#4), sequence alignment score = 2320.4
RMSD between 408 pruned atom pairs is 0.341 angstroms; (across all 435 pairs:
2.891)
Matchmaker gcgr_glucagon_model.cif, chain A (#5) with
gcgr_nnc-9204-0043_model.cif, chain A (#6), sequence alignment score = 2352.8
RMSD between 423 pruned atom pairs is 0.212 angstroms; (across all 435 pairs:
0.595)
Matchmaker gcgr_glucagon_model.cif, chain A (#5) with
gcgr_cotadutide_model.cif, chain A (#7), sequence alignment score = 2313.2
RMSD between 390 pruned atom pairs is 0.407 angstroms; (across all 435 pairs:
3.807)
Matchmaker gcgr_glucagon_model.cif, chain A (#5) with
gcgr_survodutide_model.cif, chain A (#8), sequence alignment score = 2340.2
RMSD between 395 pruned atom pairs is 0.773 angstroms; (across all 435 pairs:
3.638)
Matchmaker gcgr_glucagon_model.cif, chain A (#5) with
gcgr_retatrutide_model.cif, chain A (#9), sequence alignment score = 2320.4
RMSD between 408 pruned atom pairs is 0.341 angstroms; (across all 435 pairs:
2.891)
> hide #6 models
> hide #7 models
> hide #8 models
> hide #9 models
> hide #2 models
> hide #4 models
> hide #1 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #8 models
> lighting shadows true intensity 0.5
> lighting flat
> graphics silhouettes false
> lighting shadows true intensity 0.5
> color #5,8 bychain
> undo
> lighting flat
> hide #8 models
> color #5 bychain
> hide #5 models
> show #8 models
> color #8 byhetero
> color #8 bychain
> undo
> show #5 models
> undo
> hide #8 models
> show #5 models
> undo
> ui tool show Matchmaker
> matchmaker #1-2,4,6-9 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker gcgr_glucagon_model.cif, chain A (#5) with
gcgr_nnc-9204-1702_model.cif, chain A (#1), sequence alignment score = 2337.2
RMSD between 416 pruned atom pairs is 0.394 angstroms; (across all 435 pairs:
0.942)
Matchmaker gcgr_glucagon_model.cif, chain A (#5) with
gcgr_adomeglivant_model.cif, chain A (#2), sequence alignment score = 2310.2
RMSD between 373 pruned atom pairs is 0.806 angstroms; (across all 435 pairs:
10.796)
Matchmaker gcgr_glucagon_model.cif, chain A (#5) with
gcgr_retatrutide_model.cif, chain A (#4), sequence alignment score = 2320.4
RMSD between 408 pruned atom pairs is 0.341 angstroms; (across all 435 pairs:
2.891)
Matchmaker gcgr_glucagon_model.cif, chain A (#5) with
gcgr_nnc-9204-0043_model.cif, chain A (#6), sequence alignment score = 2352.8
RMSD between 423 pruned atom pairs is 0.212 angstroms; (across all 435 pairs:
0.595)
Matchmaker gcgr_glucagon_model.cif, chain A (#5) with
gcgr_cotadutide_model.cif, chain A (#7), sequence alignment score = 2313.2
RMSD between 390 pruned atom pairs is 0.407 angstroms; (across all 435 pairs:
3.807)
Matchmaker gcgr_glucagon_model.cif, chain A (#5) with
gcgr_survodutide_model.cif, chain A (#8), sequence alignment score = 2340.2
RMSD between 395 pruned atom pairs is 0.773 angstroms; (across all 435 pairs:
3.638)
Matchmaker gcgr_glucagon_model.cif, chain A (#5) with
gcgr_retatrutide_model.cif, chain A (#9), sequence alignment score = 2320.4
RMSD between 408 pruned atom pairs is 0.341 angstroms; (across all 435 pairs:
2.891)
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #4/A #2/A #5/A #6/A #7/A #8/A #9/A
Alignment identifier is 1
> select #1/A:1-16 #4/A:1-16 #2/A:1-16 #5/A:1-16 #6/A:1-16 #7/A:1-16 #8/A:1-16
> #9/A:1-16
1016 atoms, 1040 bonds, 128 residues, 8 models selected
> select #1/A #4/A #2/A #5/A #6/A #7/A #8/A #9/A
28176 atoms, 29024 bonds, 3480 residues, 8 models selected
. [ID: 1] region 8 chains [1-435] RMSD: 5.521
> color (#5 & sel) #d6d6d6ff
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.11rc202512030952 (2025-12-03)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M4 Max
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac16,6
Model Number: Z1FE003J3DK/A
Chip: Apple M4 Max
Total Number of Cores: 16 (12 performance and 4 efficiency)
Memory: 64 GB
System Firmware Version: 13822.41.1
OS Loader Version: 13822.41.1
Software:
System Software Overview:
System Version: macOS 26.1 (25B78)
Kernel Version: Darwin 25.1.0
Time since boot: 22 days, 22 hours, 45 minutes
Graphics/Displays:
Apple M4 Max:
Chipset Model: Apple M4 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 40
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
HP E34m G4:
Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
UI Looks like: 3440 x 1440 @ 75.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.1
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
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: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
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: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11rc202512030952
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: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
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-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
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: 1.0.1
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: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.11
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
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: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
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
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.12.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.17
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.0
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.25.1
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.2.5
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.1
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.20
pytz: 2025.2
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals-py: 3.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
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
sse-starlette: 3.0.3
stack-data: 0.6.3
starlette: 0.50.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.2
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
tzdata: 2025.2
urllib3: 2.5.0
uvicorn: 0.38.0
wcwidth: 0.2.14
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
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