id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17225 Crash on exit destroying OpenGL contexts chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.3.2-x86_64-i386-64bit ChimeraX Version: 1.10.dev202503262146 (2025-03-26 21:46:50 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 0x00007ff84afc6b00 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 440 in quit File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 805 in closeEvent File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 302 in event File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 339 in event_loop File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 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, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, 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, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, chimerax.alignment_algs._sw, chimerax.pdb._pdbio, lz4._version, lz4.frame._frame, msgpack._cmsgpack, PIL._imaging, chimerax.core._serialize, PIL._imagingmath, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atom_search.ast, chimerax.chem_group._chem_group, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 60) {""app_name"":""ChimeraX"",""timestamp"":""2025-03-27 15:54:10.00 -0400"",""app_version"":""1.10.0"",""slice_uuid"":""f855cdda-9ed8-308a-81a6-2e57ba7af811"",""build_version"":""1.10.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 15.3.2 (24D81)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""75B3A7E1-B887-443E-9992-32B7A97955E3""} { ""uptime"" : 7100, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro15,2"", ""coalitionID"" : 2722, ""osVersion"" : { ""train"" : ""macOS 15.3.2"", ""build"" : ""24D81"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-03-27 15:53:36.5400 -0400"", ""codeSigningMonitor"" : 0, ""incident"" : ""75B3A7E1-B887-443E-9992-32B7A97955E3"", ""pid"" : 1995, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2025-03-27 14:13:40.1445 -0400"", ""procStartAbsTime"" : 1166350522627, ""procExitAbsTime"" : 7162610835066, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.10.0"",""CFBundleVersion"":""1.10.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""F124C8F3-20A4-5DE1-9F07-0AC184CC1883"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""D7647BD3-ABC0-184D-0D50-636FDB066300"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""bootSessionUUID"" : ""3D97EDBA-DD48-43F3-973E-02DB4674AD89"", ""bridgeVersion"" : {""build"":""22P3060"",""train"":""9.3""}, ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0 is not in any region. Bytes before following region: 4308041728\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100c78000-100c7c000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX"", ""exception"" : {""codes"":""0x0000000000000001, 0x0000000000000000"",""rawCodes"":[1,0],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x0000000000000000""}, ""termination"" : {""flags"":0,""code"":11,""namespace"":""SIGNAL"",""indicator"":""Segmentation fault: 11"",""byProc"":""ChimeraX"",""byPid"":1995}, ""ktriageinfo"" : ""VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n"", ""vmregioninfo"" : ""0 is not in any region. 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swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=1.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.4G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG image 536K 50 \nCG raster data 44K 4 \nColorSync 260K 33 \nCoreAnimation 1264K 118 \nCoreGraphics 12K 2 \nCoreUI image data 5128K 39 \nFoundation 32K 2 \nIOKit 7940K 1 \nKernel Alloc Once 8K 1 \nMALLOC 797.9M 324 \nMALLOC guard page 48K 12 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMach message 16K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 188K 47 \nStack 286.9M 48 \nStack Guard 56.0M 1 \nVM_ALLOCATE 220.2M 166 \nVM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 43.7M 1085 \n__DATA_CONST 102.7M 1012 \n__DATA_DIRTY 2569K 341 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5176K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 214.8M 154 \n__OBJC_RO 76.9M 1 \n__OBJC_RW 2375K 2 \n__TEXT 1.4G 1101 \n__TPRO_CONST 272K 2 \ndyld private memory 80K 2 \nmapped file 579.5M 94 \nowned unmapped memory 68.2M 1 \nshared memory 3012K 32 \n=========== ======= ======= \nTOTAL 3.8G 4692 \nTOTAL, minus reserved VM space 3.8G 4692 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""876fdd2010a31ebed43feb87fdba6363a7970e14"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""5ffde50ce2aacd000d47a95f"", ""factorPackIds"" : { }, ""deploymentId"" : 240000464 }, { ""rolloutId"" : ""6425c75e4327780c10cc4252"", ""factorPackIds"" : { ""SIRI_HOME_AUTOMATION_INTENT_SELECTION_CACHE"" : ""642600a457e7664b1698eb32"" }, ""deploymentId"" : 240000004 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.10.dev202503262146 (2025-03-26) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show AlphaFold > alphafold predict > MSVVESKRKENGGSGPVTPDIGGTSLLKRESKVAKSLWLRQQDTITRLEELQRQHEEEIRAKERRQNSYDDLRTPLRSVDGSRRPSVVNDINDYRGRPLHDQLHGAYRATLLSHHTKNLNLRGFLNLFFILLFVINFRMVTDNLMEYGLMIRLPSSFRDILSNWPMLLCFLLMHFCILGAFVIERFVAAWVPHLLDWSECVLIGLNFFLVFIVPYLTVCNSSPSPAASALLLAFSIVWLFKLFSFHHVCLDARRALRDGDNFRELCSNSEEAEHVRRYPYSITLRHLYTFIWMPTMCFQFYYPRVPRIRWLSVIRHVFESAACLALMKIVVDQHIVPVARNSFTITEMQSIPLSTLLVHFLDKITRLSIPNLYVWLLMFVGLFHHWCNILAEVTRFGDRQFYLDWWNASSFGEYWRKWNLPIHHFLNRHINKPLRRARFPRIVATSVVFLISALLHEYMITVPLQLGWTGWVFLGFMAQAPLTYITNLSFFQRNPTVGNCFFWFIFCFSGQPLGILIYWYLWGVKHGTVQQLDPSKIQIM,MSVVESKRKENGGSGPVTPDIGGTSLLKRESKVAKSLWLRQQDTITRLEELQRQHEEEIRAKERRQNSYDDLRTPLRSVDGSRRPSVVNDINDYRGRPLHDQLHGAYRATLLSHHTKNLNLRGFLNLFFILLFVINFRMVTDNLMEYGLMIRLPSSFRDILSNWPMLLCFLLMHFCILGAFVIERFVAAWVPHLLDWSECVLIGLNFFLVFIVPYLTVCNSSPSPAASALLLAFSIVWLFKLFSFHHVCLDARRALRDGDNFRELCSNSEEAEHVRRYPYSITLRHLYTFIWMPTMCFQFYYPRVPRIRWLSVIRHVFESAACLALMKIVVDQHIVPVARNSFTITEMQSIPLSTLLVHFLDKITRLSIPNLYVWLLMFVGLFHHWCNILAEVTRFGDRQFYLDWWNASSFGEYWRKWNLPIHHFLNRHINKPLRRARFPRIVATSVVFLISALLHEYMITVPLQLGWTGWVFLGFMAQAPLTYITNLSFFQRNPTVGNCFFWFIFCFSGQPLGILIYWYLWGVKHGTVQQLDPSKIQIM Please cite ColabFold: Making protein folding accessible to all. Nature Methods (2022) if you use these predictions. Running AlphaFold prediction > matchmaker #5 to #1 No 'to' model specified Running AlphaFold prediction > save ""/Users/jamestyler/Desktop/CimeraX Files/testing alphafold in chimera > with Tg DGAT.cxs"" includeMaps true > open ""/Users/jamestyler/Desktop/CimeraX Files/8esm_DGAT1 with T863 > bound.pdb"" 8esm_DGAT1 with T863 bound.pdb title: Human triacylglycerol synthesizing enzyme DGAT1 In complex with T863 inhibitor [more info...] Chain information for 8esm_DGAT1 with T863 bound.pdb #1 --- Chain | Description | UniProt A B | diacylglycerol O-acyltransferase 1 | DGAT1_HUMAN 1-488 Non-standard residues in 8esm_DGAT1 with T863 bound.pdb #1 --- WS0 — {(1R,4R)-4-[4-(4-amino-7,7-dimethyl-7H-pyrimido[4,5-B][1,4]oxazin-6-yl)phenyl]cyclohexyl}acetic acid > select /A:66-481 3360 atoms, 3467 bonds, 1 pseudobond, 406 residues, 2 models selected > show sel surfaces > ui mousemode right select > select clear > ui mousemode right translate > select ::name=""WS0"" 58 atoms, 64 bonds, 2 residues, 1 model selected > ui tool show Contacts > contacts sel setAttrs true overlapCutoff 0.4 ignoreHiddenModels true select > true color #73faf8 reveal true No contacts > contacts sel setAttrs true overlapCutoff 0.20000000000000004 > ignoreHiddenModels true select true color #73faf8 reveal true No atoms match given atom specifier > select add #1 6778 atoms, 6998 bonds, 2 pseudobonds, 814 residues, 3 models selected > ui tool show Contacts > select subtract #1 1 model selected > ui mousemode right select > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 29 atoms, 32 bonds, 1 residue, 1 model selected > ui tool show Contacts > contacts sel overlapCutoff 0.2 ignoreHiddenModels true select true color > #73faf8 reveal true 6 contacts > contacts sel setAttrs true attrName overlap_0.2A overlapCutoff 0.2 > ignoreHiddenModels true select true color #73faf8 reveal true Invalid ""attrName"" argument: Attribute names can consist only of alphanumeric characters and underscores > ui tool show Contacts > contacts sel setAttrs true attrName overlap_0_2A overlapCutoff 0.2 > ignoreHiddenModels true select true color #73faf8 reveal true 6 contacts > contacts sel setAttrs true attrName overlap_0_2A overlapCutoff 0.2 > ignoreHiddenModels true select true color #73faf8 reveal true 6 contacts > select clear > select /B:501@C11 1 atom, 1 residue, 1 model selected > select up 29 atoms, 32 bonds, 1 residue, 1 model selected > ui tool show Contacts > contacts sel overlapCutoff 0.1 ignoreHiddenModels true select true color > #73faf8 reveal true 12 contacts > contacts sel overlapCutoff 0.3 ignoreHiddenModels true select true color > #73faf8 reveal true 2 contacts > select clear > color sel red > ui tool show ""Color Actions"" > select clear > select /B:407@CB 1 atom, 1 residue, 1 model selected > select up 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel red > undo > ui tool show ""Color Actions"" > color sel red target cs > select /B:411 6 atoms, 5 bonds, 1 residue, 1 model selected > ui tool show ""Color Actions"" > color sel red target cs > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 29 atoms, 32 bonds, 1 residue, 1 model selected > contacts sel overlapCutoff 0.19999999999999998 ignoreHiddenModels true > select true color #73faf8 reveal true 6 contacts > select /B:407 7 atoms, 6 bonds, 1 residue, 1 model selected > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 7 atoms, 6 bonds, 1 residue, 1 model selected > style sel sphere Changed 7 atom styles > select /B:411 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 180 atoms, 186 bonds, 22 residues, 1 model selected > select down 6 atoms, 5 bonds, 1 residue, 1 model selected > style sel sphere Changed 6 atom styles > select clear > select /B:501@C18 1 atom, 1 residue, 1 model selected > select up 29 atoms, 32 bonds, 1 residue, 1 model selected > select up 3389 atoms, 3499 bonds, 407 residues, 1 model selected > select down 29 atoms, 32 bonds, 1 residue, 1 model selected > contacts sel overlapCutoff 0.19999999999999998 ignoreHiddenModels true > select true color #73faf8 reveal true 6 contacts > ui tool show ""Color Actions"" > color sel orange target cs > select clear > select /B:408 11 atoms, 11 bonds, 1 residue, 1 model selected > select /B:407@CB 1 atom, 1 residue, 1 model selected > select up 7 atoms, 6 bonds, 1 residue, 1 model selected > style sel stick Changed 7 atom styles > ui tool show ""Color Actions"" > color sel red target cs > select /B:411 6 atoms, 5 bonds, 1 residue, 1 model selected > ui tool show ""Color Actions"" > color sel red target cs > select clear > select /B:411@CB 1 atom, 1 residue, 1 model selected > style sel stick Changed 1 atom style > select /B:411@CA 1 atom, 1 residue, 1 model selected > select up 6 atoms, 5 bonds, 1 residue, 1 model selected > style sel stick Changed 6 atom styles > select clear > contacts sel overlapCutoff 0.09999999999999998 ignoreHiddenModels true > select true color #73faf8 reveal true No atoms match given atom specifier > select /B:501@C11 1 atom, 1 residue, 1 model selected > select up 29 atoms, 32 bonds, 1 residue, 1 model selected > contacts sel overlapCutoff 0.09999999999999998 ignoreHiddenModels true > select true color #73faf8 reveal true 12 contacts > style sel sphere Changed 19 atom styles > select clear > select /B:390@CZ 1 atom, 1 residue, 1 model selected > select up 12 atoms, 12 bonds, 1 residue, 1 model selected > select up 66 atoms, 67 bonds, 7 residues, 1 model selected > select down 12 atoms, 12 bonds, 1 residue, 1 model selected > style sel stick Changed 12 atom styles > color sel yellow > undo > ui tool show ""Color Actions"" > color sel yellow target cs > select /B:375 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel yellow target cs > select /B:381@CG1 1 atom, 1 residue, 1 model selected > color sel yellow target cs > select clear > select /B:197 5 atoms, 4 bonds, 1 residue, 1 model selected > ui mousemode right translate > ui mousemode right select > select /B:501@C13 1 atom, 1 residue, 1 model selected > select up 29 atoms, 32 bonds, 1 residue, 1 model selected > select up 3389 atoms, 3499 bonds, 407 residues, 1 model selected > select down 29 atoms, 32 bonds, 1 residue, 1 model selected > style sel stick Changed 29 atom styles > contacts sel overlapCutoff 0.09999999999999998 ignoreHiddenModels true > select true color #73faf8 reveal true 12 contacts > style sel stick Changed 19 atom styles > select clear Drag select of 4 atoms, 2 residues, 4 bonds > select clear > select /B:501@C11 1 atom, 1 residue, 1 model selected > select up 29 atoms, 32 bonds, 1 residue, 1 model selected > ui tool show H-Bonds > hbonds sel color #8efa00 dashes 6 showDist true twoColors true slopColor > #ff2600 select true reveal true retainCurrent true 5 hydrogen bonds found 1 strict hydrogen bonds found > ui mousemode right translate > style sel ball Changed 7 atom styles > hide #1.4.1 models > ui mousemode right select > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 29 atoms, 32 bonds, 1 residue, 1 model selected > ui tool show H-Bonds > hbonds sel color #8efa00 dashes 6 showDist true twoColors true slopColor > #ff2600 select true reveal true retainCurrent true 5 hydrogen bonds found 1 strict hydrogen bonds found > select clear > hide #1.2 models > select /A:411 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel lime target cs > select /A:378 8 atoms, 7 bonds, 1 residue, 1 model selected > style sel stick Changed 8 atom styles > hide sel cartoons > show sel cartoons > hide (#!1 & sel-residues & (protein|nucleic)) target a > cartoon hide (#!1 & sel-residues) > show (#!1 & sel-residues & backbone) target ab > show sel cartoons > ui mousemode right translate > cartoon (#!1 & sel) > show (#!1 & sel) target ab > hide sel atoms > ui tool show ""Color Actions"" > color sel yellow target cs > ui mousemode right select > select /A:374 14 atoms, 15 bonds, 1 residue, 1 model selected > color sel yellow target cs > select /A:377 14 atoms, 15 bonds, 1 residue, 1 model selected > color sel yellow target cs > show #1.4.1 models > select clear > ui mousemode right translate > show #1.2 models > save ""/Users/jamestyler/Desktop/CimeraX Files/8esm_DGAT1 with T863 bound and > contacts colored.cxs"" includeMaps true > close #1 > open 6pvo format mmcif fromDatabase pdb 6pvo title: Cryo-EM structure of mouse TRPV3-Y564A in putative sensitized state at 37 degrees Celsius [more info...] Chain information for 6pvo #1 --- Chain | Description | UniProt A B C D | Transient receptor potential cation channel subfamily V member 3 | TRPV3_MOUSE 1-791 > close > open /Users/jamestyler/Downloads/6vp0.pdb 6vp0.pdb title: Human diacylglycerol acyltransferase 1 In complex with oleoyl-coa [more info...] Chain information for 6vp0.pdb #1 --- Chain | Description | UniProt C E | diacylglycerol O-acyltransferase 1 | DGAT1_HUMAN 1-488 Non-standard residues in 6vp0.pdb #1 --- 3VV — S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3Λ~5~,5Λ~5~-diphosphaheptadecan-17-yl} (9Z)-octadec-9-enethioate(non-preferred name) (oleoyl-coa) AV0 — lauryl maltose neopentyl glycol (2,2-didecylpropane-1,3-bis-B-D- maltopyranoside; 2-decyl-2-{[(4-O-α-D-glucopyranosyl-β-D- glucopyranosyl)oxy]methyl}DODECYL4-O-α-D-glucopyranosyl-β-D-glucopyranoside) P5S — O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine (phosphatidyl serine) POV — (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (POPC) > select ::name=""POV"" 140 atoms, 136 bonds, 4 residues, 1 model selected > select add #1 7210 atoms, 7422 bonds, 2 pseudobonds, 820 residues, 3 models selected > select subtract #1 Nothing selected > select add #1 7210 atoms, 7422 bonds, 2 pseudobonds, 820 residues, 3 models selected Alignment identifier is 1 > ui mousemode right select > select clear > select /C-E:404 22 atoms, 20 bonds, 2 residues, 1 model selected > select /C-E:404 22 atoms, 20 bonds, 2 residues, 1 model selected > style sel sphere Changed 22 atom styles > select clear > select /C-E:400 18 atoms, 16 bonds, 2 residues, 1 model selected > select /C-E:400 18 atoms, 16 bonds, 2 residues, 1 model selected > style sel sphere Changed 18 atom styles > select clear > select /C-E:390 24 atoms, 24 bonds, 2 residues, 1 model selected > select /C-E:390 24 atoms, 24 bonds, 2 residues, 1 model selected > style sel sphere Changed 24 atom styles > select /C-E:382 20 atoms, 20 bonds, 2 residues, 1 model selected > select /C-E:382 20 atoms, 20 bonds, 2 residues, 1 model selected > style sel sphere Changed 20 atom styles > select /C-E:375 18 atoms, 16 bonds, 2 residues, 1 model selected > select /C-E:375 18 atoms, 16 bonds, 2 residues, 1 model selected > style sel sphere Changed 18 atom styles > select clear > select /C-E:371 14 atoms, 12 bonds, 2 residues, 1 model selected > select /C-E:371 14 atoms, 12 bonds, 2 residues, 1 model selected > style sel sphere Changed 14 atom styles > show sel atoms > select clear > select /C-E:371 14 atoms, 12 bonds, 2 residues, 1 model selected > select /C-E:371 14 atoms, 12 bonds, 2 residues, 1 model selected > select /C-E:375 18 atoms, 16 bonds, 2 residues, 1 model selected > select /C-E:375 18 atoms, 16 bonds, 2 residues, 1 model selected > select /C-E:382 20 atoms, 20 bonds, 2 residues, 1 model selected > select /C-E:382 20 atoms, 20 bonds, 2 residues, 1 model selected > select /C-E:371 14 atoms, 12 bonds, 2 residues, 1 model selected > select /C-E:375 18 atoms, 16 bonds, 2 residues, 1 model selected > select /C-E:382 20 atoms, 20 bonds, 2 residues, 1 model selected > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 67 atoms, 69 bonds, 1 residue, 1 model selected > ui tool show H-Bonds > hbonds sel color #8efa00 dashes 6 showDist true twoColors true slopColor > #ff2600 select true reveal true retainCurrent true 7 hydrogen bonds found 2 strict hydrogen bonds found > select clear > select /E:371@CG2 1 atom, 1 residue, 1 model selected > select clear > select /E:371@CB 1 atom, 1 residue, 1 model selected > select up 7 atoms, 6 bonds, 1 residue, 1 model selected > style sel ball Changed 7 atom styles > select /E:375@CG 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 1 model selected > style sel ball Changed 9 atom styles > select /E:382@NE2 1 atom, 1 residue, 1 model selected > select up 10 atoms, 10 bonds, 1 residue, 1 model selected > style sel ball Changed 10 atom styles > select /E:400@CD 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 1 model selected > style sel ball Changed 9 atom styles > select /E:404@NH1 1 atom, 1 residue, 1 model selected > select up 11 atoms, 10 bonds, 1 residue, 1 model selected > style sel ball Changed 11 atom styles > select /E:390@CE2 1 atom, 1 residue, 1 model selected > select up 12 atoms, 12 bonds, 1 residue, 1 model selected > style sel ball Changed 12 atom styles > select clear > ui mousemode right translate > save ""/Users/jamestyler/Desktop/CimeraX Files/6vp0 DGAT1_Hbonds and paper > contacts balled.cxs"" includeMaps true > close ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.10.dev202503262146 (2025-03-26) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-23.0.22 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655 OpenGL vendor: Intel Inc. Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro15,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 2069.80.3.0.0 (iBridge: 22.16.13060.0.0,0) OS Loader Version: 582~3311 Software: System Software Overview: System Version: macOS 15.3.2 (24D81) Kernel Version: Darwin 24.3.0 Time since boot: 2 hours, 18 minutes Graphics/Displays: Intel Iris Plus Graphics 655: Chipset Model: Intel Iris Plus Graphics 655 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3ea5 Revision ID: 0x0001 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: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.3.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.2.1 build: 1.2.2.post1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.1 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.19.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.1 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.5 ChimeraX-AtomicLibrary: 14.1.13 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10.dev202503262146 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5.1 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.5.3 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.7 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-ProfileGrids: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.1 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.45 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 coverage: 7.7.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.13 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.56.0 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h5py: 3.13.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.1.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.1.0 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 24.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.0.1 pkginfo: 1.11.1 platformdirs: 4.3.7 pluggy: 1.5.0 prompt_toolkit: 3.0.50 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.32 Pygments: 2.18.0 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.3 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.2 PyQt6_sip: 13.10.0 pytest: 8.3.5 pytest-cov: 6.0.0 python-dateutil: 2.9.0.post0 pytz: 2025.2 pyzmq: 26.3.0 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 roman-numerals-py: 3.1.0 scipy: 1.14.0 setuptools: 75.8.2 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.1.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.7.1 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.13.0 tzdata: 2025.2 urllib3: 2.3.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.13 }}} " defect closed normal Graphics can't reproduce all ChimeraX