id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19504 Crash during window geometry change in QDockWidget::event() chimerax-bug-report@… Tom Goddard "{{{ 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) {""app_name"":""ChimeraX"",""timestamp"":""2025-12-10 09:25:51.00 +0100"",""app_version"":""1.11.0"",""slice_uuid"":""c20e09a8-923e-3fb3-856b-3e765bcb267b"",""build_version"":""1.11.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 26.1 (25B78)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""D99F2F16-3ACF-45EC-B46A-BF1AEFCEA0E3""} { ""uptime"" : 630000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""Mac16,6"", ""coalitionID"" : 76772, ""osVersion"" : { ""train"" : ""macOS 26.1"", ""build"" : ""25B78"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-12-10 09:25:40.9321 +0100"", ""codeSigningMonitor"" : 2, ""incident"" : ""D99F2F16-3ACF-45EC-B46A-BF1AEFCEA0E3"", ""pid"" : 87010, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2025-12-09 15:03:24.5677 +0100"", ""procStartAbsTime"" : 14004468665008, ""procExitAbsTime"" : 15331483500165, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.11-rc2025.12.03.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.11.0"",""CFBundleVersion"":""1.11.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""FF700023-352E-5172-9683-AA6F7267F293"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""5E066A44-CF6C-F7B2-9D5E-E368EF041886"", ""appleIntelligenceStatus"" : {""state"":""available""}, ""developerMode"" : 1, ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""codeSigningAuxiliaryInfo"" : 0, ""instructionByteStream"" : {""beforePC"":""fyMD1f17v6n9AwCRFOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A=="",""atPC"":""AwEAVH8jA9X9e7+p\/QMAkQng\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g==""}, ""bootSessionUUID"" : ""96B2468E-8866-4F80-977E-2A84218DC281"", ""wakeTime"" : 2116, ""sleepWakeUUID"" : ""C09A0B02-101C-4FEF-A3F7-D29979150EBF"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x8 is not in any region. 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""0d8bfe9374e1433fd1dbf25c94e2ed4a1ab10887"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""65a8173205d942272410674b"", ""factorPackIds"" : [ ""65d39fa4cb0e2417d11ce5f6"" ], ""deploymentId"" : 240000001 }, { ""rolloutId"" : ""661464ecda55e5192b100804"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000005 } ], ""experiments"" : [ { ""treatmentId"" : ""28060e10-d4e5-4163-aa2b-d8bd088d5cbf"", ""experimentId"" : ""6685b283afc7c17197d69eec"", ""deploymentId"" : 400000012 } ] } } ===== 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 }}} " defect closed normal Window Toolkit can't reproduce all ChimeraX