id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20375 Crash in QObject::event chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-13.7.8-x86_64-i386-64bit ChimeraX Version: 1.12rc202605080108 (2026-05-08 01:08:27 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x000070001c0a8000 (most recent call first): File ""/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 331 in wait File ""/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 629 in wait File ""/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1399 in run File ""/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Current thread 0x00007ff847bbea00 (most recent call first): File ""/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 424 in event_loop File ""/Applications/ChimeraX-1.12-rc2026.05.08.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-1.12-rc2026.05.08.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, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb_lib._load_libs, chimerax.map._map, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, PIL._imaging, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, kiwisolver._cext, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 56) {""app_name"":""ChimeraX"",""timestamp"":""2026-05-21 19:31:11.00 +0100"",""app_version"":""1.12.0"",""slice_uuid"":""5cbc32a0-c22e-3696-af85-4071e4699df0"",""build_version"":""1.12.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 13.7.8 (22H730)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""A6A74942-D7D8-4A3C-8CD1-D64E560002B6""} { ""uptime"" : 140000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro14,1"", ""coalitionID"" : 477, ""osVersion"" : { ""train"" : ""macOS 13.7.8"", ""build"" : ""22H730"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2026-05-21 19:31:03.1172 +0100"", ""incident"" : ""A6A74942-D7D8-4A3C-8CD1-D64E560002B6"", ""pid"" : 40817, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2026-05-21 09:31:05.2819 +0100"", ""procStartAbsTime"" : 128228169410608, ""procExitAbsTime"" : 148472166496220, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.12-rc2026.05.08.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.12.0"",""CFBundleVersion"":""1.12.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""94A64494-2CCA-5044-99AB-8FB03D2938BD"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""AD5DAD3F-C80E-DE82-9804-D336B5F757D7"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 0, ""wakeTime"" : 2936, ""sleepWakeUUID"" : ""814E32DB-9EC7-45D4-8753-9A1A018B007A"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0 is not in any region. 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""logWritingSignature"" : ""4a6fd6d0121a379ae32f62f2efa86808aceef6c6"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""64c17a9925d75a7281053d4c"", ""factorPackIds"" : { ""SIRI_AUDIO_DISABLE_MEDIA_ENTITY_SYNC"" : ""64d29746ad29a465b3bbeace"" }, ""deploymentId"" : 240000002 }, { ""rolloutId"" : ""5ffde50ce2aacd000d47a95f"", ""factorPackIds"" : { }, ""deploymentId"" : 240000533 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.12rc202605080108 (2026-05-08) © 2016-2026 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/asmaalhelal/Downloads/fold_2026_05_20_parb_4_copies/fold_2026_05_20_parb_4_copies_model_0.cif Chain information for fold_2026_05_20_parb_4_copies_model_0.cif #1 --- Chain | Description A B C D | . Computing secondary structure > open > /Users/asmaalhelal/Downloads/fold_2026_05_20_parb_4_copies/fold_2026_05_20_parb_4_copies_model_0.cif Chain information for fold_2026_05_20_parb_4_copies_model_0.cif #2 --- Chain | Description A B C D | . Computing secondary structure > ui tool show Toolbar > color bychain > close #2 > interfaces ~solvent 3 buried areas: A B 1618, C D 1614, B C 383 > hbonds sel reveal true 12 hydrogen bonds found > ui mousemode right zoom > ui tool show Contacts > contacts sel intraModel false intraMol false ignoreHiddenModels true reveal > true log true Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: False 0 contacts atom1 atom2 overlap distance No contacts > hbonds sel reveal true 27 hydrogen bonds found > open > /Users/asmaalhelal/Downloads/ChimeraX/ParA/fold_2026_03_20_para_atp/fold_2026_03_20_para_atp_model_4.cif Chain information for fold_2026_03_20_para_atp_model_4.cif #2 --- Chain | Description A B | . Computing secondary structure > close #1 > open > /Users/asmaalhelal/Downloads/ChimeraX/ParA/fold_2026_03_20_para_atp/fold_2026_03_20_para_atp_model_3.cif Chain information for fold_2026_03_20_para_atp_model_3.cif #1 --- Chain | Description A B | . Computing secondary structure > hide #2 models > close #1 > open > /Users/asmaalhelal/Downloads/ChimeraX/ParA/fold_2026_03_20_para_atp/fold_2026_03_20_para_atp_model_2.cif Chain information for fold_2026_03_20_para_atp_model_2.cif #1 --- Chain | Description A B | . Computing secondary structure > close #1 > open > /Users/asmaalhelal/Downloads/ChimeraX/ParA/fold_2026_03_20_para_atp/fold_2026_03_20_para_atp_model_1.cif Chain information for fold_2026_03_20_para_atp_model_1.cif #1 --- Chain | Description A B | . Computing secondary structure > close #1 > open > /Users/asmaalhelal/Downloads/ChimeraX/ParA/fold_2026_03_20_para_atp/fold_2026_03_20_para_atp_model_0.cif Chain information for fold_2026_03_20_para_atp_model_0.cif #1 --- Chain | Description A B | . Computing secondary structure > close #1 > show #2 models > sequence chain #2/A,B Alignment identifier is 1 > select /A-B:9 18 atoms, 16 bonds, 2 residues, 1 model selected > select /A-B:9 18 atoms, 16 bonds, 2 residues, 1 model selected > color sel byelement > style sel ball Changed 18 atom styles > set bgColor white > select add #2 3356 atoms, 3404 bonds, 430 residues, 1 model selected > select subtract #2 Nothing selected > color bfactor #1/A palette alphafold No atoms specified > color bfactor #2/A palette alphafold 1647 atoms, 214 residues, atom bfactor range 36.2 to 98.7 > color #009051ff > color #558d6fff > color #68ad87ff > color bfactor #2/A palette alphafold 1647 atoms, 214 residues, atom bfactor range 36.2 to 98.7 > select add #2 3356 atoms, 3404 bonds, 430 residues, 1 model selected > color sel byelement > select subtract #2 Nothing selected > select /A-B:9 18 atoms, 16 bonds, 2 residues, 1 model selected > select /A-B:9 18 atoms, 16 bonds, 2 residues, 1 model selected > style sel sphere Changed 18 atom styles > style sel ball Changed 18 atom styles > select add #2 3356 atoms, 3404 bonds, 430 residues, 1 model selected > select subtract #2 Nothing selected > open 1P94 fromDatabase pdbe_bio format mmcif Summary of feedback from opening 1P94 fetched from pdbe_bio --- warnings | Previously completed PDB model 1 found. Trying to extend. Previously completed PDB model 2 found. Trying to extend. Previously completed PDB model 3 found. Trying to extend. Previously completed PDB model 4 found. Trying to extend. Previously completed PDB model 5 found. Trying to extend. 6 messages similar to the above omitted Missing or incorrect sequence information. Inferred polymer connectivity. subunit 1 title: NMR Structure of ParG symmetric dimer [more info...] Chain information for subunit 1 #1.1 --- Chain | Description A B | plasmid partition protein ParG Chain information for subunit 2 #1.2 --- Chain | Description A B | plasmid partition protein ParG Chain information for subunit 3 #1.3 --- Chain | Description A B | plasmid partition protein ParG Chain information for subunit 4 #1.4 --- Chain | Description A B | plasmid partition protein ParG Chain information for subunit 5 #1.5 --- Chain | Description A B | plasmid partition protein ParG Chain information for subunit 6 #1.6 --- Chain | Description A B | plasmid partition protein ParG Chain information for subunit 7 #1.7 --- Chain | Description A B | plasmid partition protein ParG Chain information for subunit 8 #1.8 --- Chain | Description A B | plasmid partition protein ParG Chain information for subunit 9 #1.9 --- Chain | Description A B | plasmid partition protein ParG Chain information for subunit 10 #1.10 --- Chain | Description A B | plasmid partition protein ParG Chain information for subunit 11 #1.11 --- Chain | Description A B | plasmid partition protein ParG Opened 1 biological assemblies for 1P94 Computing secondary structure > close #1 > open 4E09 fromDatabase pdbe_bio format mmcif Summary of feedback from opening 4E09 fetched from pdbe_bio --- warning | Missing or incorrect sequence information. Inferred polymer connectivity. 4E09 bioassembly 1 title: Structure of ParF-AMPPCP, I422 form [more info...] Chain information for 4E09 bioassembly 1 #1 --- Chain | Description A AA | Plasmid partitioning protein ParF Non-standard residues in 4E09 bioassembly 1 #1 --- ACP — (ACP) SO4 — (SO4) 4E09 bioassembly 1 mmCIF Assemblies --- 1| author_and_software_defined_assembly Opened 1 biological assemblies for 4E09 Computing secondary structure > ui tool show Matchmaker > matchmaker #2 to #1 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 4E09 bioassembly 1, chain A (#1) with fold_2026_03_20_para_atp_model_4.cif, chain A (#2), sequence alignment score = 268.1 RMSD between 145 pruned atom pairs is 1.045 angstroms; (across all 197 pairs: 2.861) > ui mousemode right ""move picked models"" > view matrix models > #2,-0.23204,-0.38002,0.8954,29.598,0.9221,-0.379,0.078104,14.304,0.30967,0.84377,0.43836,36.586 > ui mousemode right ""translate selected models"" > ui mousemode right ""move picked models"" > ui mousemode right zoom > ui tool show Matchmaker > matchmaker #2 to #1 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 4E09 bioassembly 1, chain A (#1) with fold_2026_03_20_para_atp_model_4.cif, chain A (#2), sequence alignment score = 268.1 RMSD between 145 pruned atom pairs is 1.045 angstroms; (across all 197 pairs: 2.861) > hide #2 models > show #2 models > hide #!1 models > select add #2 3356 atoms, 3404 bonds, 430 residues, 1 model selected > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > select subtract #2 Nothing selected > interfaces #2 & ~solvent 3 buried areas: A B 1273, B D 392, A C 391 > ui tool show Contacts > contacts sel intraModel false intraMol false ignoreHiddenModels true reveal > true log true Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: False 0 contacts atom1 atom2 overlap distance No contacts > hbonds sel reveal true 55 hydrogen bonds found > ui mousemode right ""move picked models"" > view matrix models > #2,-0.23204,-0.38002,0.8954,31.04,0.9221,-0.379,0.078104,17.644,0.30967,0.84377,0.43836,41.227 > show #!1 models > hide #!1 models > select subtract #3 184 atoms, 23 residues, 1 model selected > select add #2 3356 atoms, 3404 bonds, 36 pseudobonds, 430 residues, 2 models selected > select subtract #2 Nothing selected > ui mousemode right select > select clear > select #2/A:154 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel > select clear > select #2/A:110 6 atoms, 5 bonds, 1 residue, 1 model selected > hide sel > select #2/A:139 6 atoms, 5 bonds, 1 residue, 1 model selected > hide sel > select clear > hide sel > select #2/A:199 5 atoms, 4 bonds, 1 residue, 1 model selected > hide sel > select #2/A:186 6 atoms, 5 bonds, 1 residue, 1 model selected > hide sel > select #2/A:145 7 atoms, 6 bonds, 1 residue, 1 model selected > hide sel > select #2/A:140 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:176 6 atoms, 5 bonds, 1 residue, 1 model selected > hide sel > select #2/A:177 11 atoms, 11 bonds, 1 residue, 1 model selected > hide sel > select #2/A:178 11 atoms, 10 bonds, 1 residue, 1 model selected > hide sel > select #2/A:38 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel > select #2/A:179 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel > select #2/A:183 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel > select #2/A:116 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel > select #2/A:112 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel > select #2/A:152 4 atoms, 3 bonds, 1 residue, 1 model selected > hide sel > select #2/A:12 6 atoms, 5 bonds, 1 residue, 1 model selected > hide sel > ui mousemode right zoom > hide #3 models > hide #4 models > show #!1 models > hide #2 models > show #2 models > ui tool show Matchmaker > matchmaker #2 to #1 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 4E09 bioassembly 1, chain A (#1) with fold_2026_03_20_para_atp_model_4.cif, chain A (#2), sequence alignment score = 268.1 RMSD between 145 pruned atom pairs is 1.045 angstroms; (across all 197 pairs: 2.861) > hide #!1 models > show #!1 models > style sphere Changed 6490 atom styles > select #1/A:1-206 1531 atoms, 1549 bonds, 1 pseudobond, 204 residues, 2 models selected > hide sel cartoons > select #2/A:1-214 1647 atoms, 1669 bonds, 27 pseudobonds, 214 residues, 2 models selected > hide sel cartoons > style sel stick Changed 1647 atom styles > style sel sphere Changed 1647 atom styles > select subtract #3 1647 atoms, 1669 bonds, 27 pseudobonds, 214 residues, 2 models selected > select add #4 1647 atoms, 1669 bonds, 55 pseudobonds, 214 residues, 2 models selected > select add #2 3356 atoms, 3404 bonds, 55 pseudobonds, 430 residues, 2 models selected > select subtract #4 3356 atoms, 3404 bonds, 430 residues, 1 model selected > select subtract #3 3356 atoms, 3404 bonds, 430 residues, 1 model selected > select subtract #2 Nothing selected > style stick Changed 6490 atom styles > select #1.11/A:1-76 Nothing selected > select #1.11/B:1-76 Nothing selected > select #1.11/A:1-76 Nothing selected > select #1/A:1-206 1531 atoms, 1549 bonds, 1 pseudobond, 204 residues, 2 models selected > hide sel atoms > select #1/A:1-214 1531 atoms, 1549 bonds, 1 pseudobond, 204 residues, 2 models selected > select #1/A:1-214 1531 atoms, 1549 bonds, 1 pseudobond, 204 residues, 2 models selected > select #1/B:1-214 Nothing selected > select #1/A:1-214 1531 atoms, 1549 bonds, 1 pseudobond, 204 residues, 2 models selected > select #2/A:1-214 1647 atoms, 1669 bonds, 27 pseudobonds, 214 residues, 2 models selected > hide sel atoms > hide #2 models > select #1.4/A:1-76 Nothing selected > select #2/A:1-214 1647 atoms, 1669 bonds, 27 pseudobonds, 214 residues, 2 models selected > show #2 models > hide #!1 models > select #2/B:1-214 1647 atoms, 1669 bonds, 214 residues, 1 model selected > select #2/B:1-214 1647 atoms, 1669 bonds, 214 residues, 1 model selected > select #2/A:1-214 1647 atoms, 1669 bonds, 27 pseudobonds, 214 residues, 2 models selected > show sel cartoons > show sel atoms > hide sel atoms > select #1/A:1-206 1531 atoms, 1549 bonds, 1 pseudobond, 204 residues, 2 models selected > select #1/A:1-206 1531 atoms, 1549 bonds, 1 pseudobond, 204 residues, 2 models selected > select #1/A:1-206 1531 atoms, 1549 bonds, 1 pseudobond, 204 residues, 2 models selected > select #2/A:1-214 1647 atoms, 1669 bonds, 27 pseudobonds, 214 residues, 2 models selected > select add #2 3356 atoms, 3404 bonds, 36 pseudobonds, 430 residues, 2 models selected > hide sel cartoons > hide sel atoms > show sel atoms > show sel cartoons > hide sel atoms > select subtract #3 3356 atoms, 3404 bonds, 36 pseudobonds, 430 residues, 2 models selected > select add #4 3356 atoms, 3404 bonds, 55 pseudobonds, 430 residues, 2 models selected > select subtract #4 3356 atoms, 3404 bonds, 430 residues, 1 model selected > select subtract #3 3356 atoms, 3404 bonds, 430 residues, 1 model selected > select #2/A-B:9 18 atoms, 16 bonds, 2 residues, 1 model selected > select #2/A-B:9 18 atoms, 16 bonds, 2 residues, 1 model selected > select add #2 3356 atoms, 3404 bonds, 36 pseudobonds, 430 residues, 2 models selected > select #2/A:1-214 1647 atoms, 1669 bonds, 27 pseudobonds, 214 residues, 2 models selected > select #2/A:1-214 1647 atoms, 1669 bonds, 27 pseudobonds, 214 residues, 2 models selected > select add #2 3356 atoms, 3404 bonds, 36 pseudobonds, 430 residues, 2 models selected > select subtract #2 Nothing selected > ui mousemode right ""move label"" > select add #2 3356 atoms, 3404 bonds, 36 pseudobonds, 430 residues, 2 models selected > select subtract #3 3356 atoms, 3404 bonds, 36 pseudobonds, 430 residues, 2 models selected > select add #4 3356 atoms, 3404 bonds, 55 pseudobonds, 430 residues, 2 models selected > ui mousemode right ""move label"" > ui mousemode right label > ui mousemode right ""move label"" > select ::name=""ATP"" 62 atoms, 66 bonds, 2 residues, 1 model selected > show sel atoms > hide sel atoms > show sel atoms > select add #2 3356 atoms, 3404 bonds, 36 pseudobonds, 430 residues, 2 models selected > select subtract #2 Nothing selected > select #2/A-B:9 18 atoms, 16 bonds, 2 residues, 1 model selected > select #2/A-B:9 18 atoms, 16 bonds, 2 residues, 1 model selected > hide sel atoms > style sel ball Changed 18 atom styles > show sel atoms > select add #2 3356 atoms, 3404 bonds, 36 pseudobonds, 430 residues, 2 models selected > select subtract #2 Nothing selected > ui mousemode right ""move picked models"" > view matrix models > #2,-0.23204,-0.38002,0.8954,35.891,0.9221,-0.379,0.078104,17.698,0.30967,0.84377,0.43836,47.328 > ui mousemode right zoom > ui mousemode right ""move picked models"" > view matrix models > #2,-0.23204,-0.38002,0.8954,40.469,0.9221,-0.379,0.078104,17.016,0.30967,0.84377,0.43836,45.08 > hide #2 models > show #!1 models > select add #1 3134 atoms, 3172 bonds, 2 pseudobonds, 412 residues, 2 models selected > show sel cartoons > select subtract #1 Nothing selected > view matrix models #1,1,0,0,1.5535,0,1,0,2.1295,0,0,1,-1.3126 > show #2 models > hide #2/A > select #2/A 1647 atoms, 1669 bonds, 27 pseudobonds, 214 residues, 2 models selected > hide sel cartoons > select #1/A 1531 atoms, 1549 bonds, 1 pseudobond, 204 residues, 2 models selected > hide sel cartoons > select ::name=""ACP"" 62 atoms, 66 bonds, 2 residues, 1 model selected > select add #1 3134 atoms, 3172 bonds, 2 pseudobonds, 412 residues, 2 models selected > select subtract #1 Nothing selected > select :ACP 62 atoms, 66 bonds, 2 residues, 1 model selected > select :ACP 62 atoms, 66 bonds, 2 residues, 1 model selected ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.12rc202605080108 (2026-05-08) © 2016-2026 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-20.7.3 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640 OpenGL vendor: Intel Inc. Python: 3.11.9 Locale: UTF-8 Qt version: PyQt6 6.10.2, Qt 6.10.0 Qt runtime version: 6.10.1 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro14,1 Processor Name: Dual-Core Intel Core i5 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 4 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 529.140.2.0.0 OS Loader Version: 577.140.2~30 SMC Version (system): 2.43f11 Software: System Software Overview: System Version: macOS 13.7.8 (22H730) Kernel Version: Darwin 22.6.0 Time since boot: 3 days, 7 hours, 12 minutes Graphics/Displays: Intel Iris Plus Graphics 640: Chipset Model: Intel Iris Plus Graphics 640 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x5926 Revision ID: 0x0006 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: accessible-pygments: 0.0.5 aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.13.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 26.1.0 babel: 2.18.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 4.2.0 bs4: 0.0.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.7 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.2 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.2 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: 1.67.1 ChimeraX-AtomicLibrary: 14.4 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: 1.4.1 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.4 ChimeraX-Cluster: 1.0 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.1 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.12rc202605080108 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: 1.2.1 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: 1.8.2 ChimeraX-Label: 1.5 ChimeraX-LightingGUI: 1.0 ChimeraX-ListInfo: 1.3.1 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.3 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-MatchAlign: 1.1 ChimeraX-MatchMaker: 2.4 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.2.0 ChimeraX-MDcrds: 2.19 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.8 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.23 ChimeraX-ModelPanel: 1.6.1 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: 1.0.1 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: 1.15.4 ChimeraX-OpenFold: 1.0 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.13 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: 1.6 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.8.2 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: 3.5.12 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.18 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-SNFG: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.3 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: 2.5.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.4 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.50.6 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.6.2 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: 8.3.3 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.5 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.2.4 debugpy: 1.8.20 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.62.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.16.0 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.13 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 2.0.0 iniconfig: 2.3.0 ipykernel: 7.1.0 ipython: 9.9.0 ipython_pygments_lexers: 1.1.1 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.8.0 jupyter_core: 5.9.1 kiwisolver: 1.5.0 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: 6.7.1 narwhals: 2.20.0 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: 8.4.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.7 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: 4.9.6 plotly: 6.7.0 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: 2.13.4 pydantic-settings: 2.14.0 pydantic_core: 2.46.4 pydata-sphinx-theme: 0.17.1 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.5.1 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.10.2 PyQt6-Qt6: 6.10.1 PyQt6-WebEngine-commercial: 6.10.0 PyQt6-WebEngine-Qt6: 6.10.1 PyQt6_sip: 13.10.3 pytest: 9.0.3 pytest-cov: 7.1.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.2 python-multipart: 0.0.27 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.1.0 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: 2.8.3 Sphinx: 9.0.4 sphinx-autodoc-typehints: 3.6.1 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: 3.4.2 stack-data: 0.6.3 starlette: 1.0.0 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 3.2.1 threadpoolctl: 3.6.0 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.5 tqdm: 4.67.3 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 Unidecode: 1.4.0 urllib3: 2.7.0 uvicorn: 0.46.0 wcwidth: 0.7.0 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 yarl: 1.23.0 }}} " defect closed normal Window Toolkit duplicate chimerax-programmers all ChimeraX