id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17205 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.6-arm64-arm-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 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 0x00000001f0884f40 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 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.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lxml._elementpath, lxml.etree (total: 61) {""app_name"":""ChimeraX"",""timestamp"":""2025-03-26 17:11:53.00 +0100"",""app_version"":""1.8.0"",""slice_uuid"":""17982d98-65bc-3327-8526-577ec996453c"",""build_version"":""1.8.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 14.6 (23G80)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""76871F46-9303-4C6D-BDC5-A3F5CBF2A9D8""} { ""uptime"" : 250000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 502, ""deployVersion"" : 210, ""modelCode"" : ""Mac15,12"", ""coalitionID"" : 7364, ""osVersion"" : { ""train"" : ""macOS 14.6"", ""build"" : ""23G80"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-03-26 17:11:48.1953 +0100"", ""codeSigningMonitor"" : 1, ""incident"" : ""76871F46-9303-4C6D-BDC5-A3F5CBF2A9D8"", ""pid"" : 52412, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2025-03-25 20:35:31.8146 +0100"", ""procStartAbsTime"" : 5282227691383, ""procExitAbsTime"" : 6174999418657, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.8.0"",""CFBundleVersion"":""1.8.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""74DC2FB7-DFB9-5D3B-92C7-63DE63B9BB3B"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""E2021406-A73F-75E2-1BEE-B7EC748CF3F3"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""instructionByteStream"" : {""beforePC"":""fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A=="",""atPC"":""AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g==""}, ""wakeTime"" : 1, ""sleepWakeUUID"" : ""315D283B-8565-452C-A0C9-5E050F4EEB5D"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x13664eb62738 is not in any region. 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All rights reserved. How to cite UCSF ChimeraX > open /Users/sara.buscarini/Desktop/Phd/PDB/5il0.pdb 5il0.pdb title: Crystal structural of the METTL3-METTL14 complex for N6-adenosine methylation [more info...] Chain information for 5il0.pdb #1 --- Chain | Description | UniProt A | METTL3 | MTA70_HUMAN 369-580 B | methyltransferase-LIKE protein 14 | MET14_HUMAN 109-408 Non-standard residues in 5il0.pdb #1 --- BR — bromide ion EDO — 1,2-ethanediol (ethylene glycol) > color #1/A #f27a93ff > color #1/B #fcbe7cff > open /Users/sara.buscarini/Desktop/Phd/PDB/5il1.pdb 5il1.pdb title: Crystal structure of sam-bound METTL3-METTL14 complex [more info...] Chain information for 5il1.pdb #2 --- Chain | Description | UniProt A | METTL3 | MTA70_HUMAN 369-580 B | methyltransferase-LIKE protein 14 | MET14_HUMAN 109-408 Non-standard residues in 5il1.pdb #2 --- EDO — 1,2-ethanediol (ethylene glycol) SAM — S-adenosylmethionine > hide #!1 models > show #!2 surfaces > select add #2 4336 atoms, 4102 bonds, 1 pseudobond, 828 residues, 2 models selected > show sel cartoons > color #2/A #f27a93ff > show #!2 target m > view #2 clip false > hide sel surfaces > select subtract #2 2 models selected > color #2/B #fcbe7cff > select #2/SAM Nothing selected > select #2/A:SAM 27 atoms, 29 bonds, 1 residue, 1 model selected > color #2/A:SAM green > style sel stick Changed 27 atom styles > color sel byhetero > select #2/A:511 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/A:SAM 27 atoms, 29 bonds, 1 residue, 1 model selected > hbonds sel reveal true 18 hydrogen bonds found > hbonds sel showDist true 18 hydrogen bonds found > color #2/A:511 red > ui tool show Distances > select #2/A:511@OG 1 atom, 1 residue, 1 model selected > select #2/A:601@OXT 1 atom, 1 residue, 1 model selected > select add #2/A:511@OG 2 atoms, 2 residues, 1 model selected > distance #2/A:601@OXT #2/A:511@OG Distance between 5il1.pdb #2/A SAM 601 OXT and SER 511 OG: 4.585Å > color #2/A:426 red > color #2/A:411 red > color #2/A:397 red > select #2/A:397 red Expected a keyword > select #2/A:397 red Expected a keyword > select #2/A:397 7 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:397 7 atoms, 7 bonds, 1 residue, 1 model selected > color #2/A:425 red > select #2/A:425 8 atoms, 7 bonds, 1 residue, 1 model selected > color #2/A:402 red > color #2/A:516 red > select #2/A:516 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:515 8 atoms, 7 bonds, 1 residue, 1 model selected > color #2/A:515 red > color #2/A:546 red > color #2/A:4 red > select #2/A:4 Nothing selected > color #2/A:438 red > open > /Users/sara.buscarini/Desktop/ligands_METTL3:14/Antonio_Sara_ligands.cxs opened ChimeraX session > hide #!5 models > ui tool show ""Side View"" > select add #2 4336 atoms, 4102 bonds, 20 pseudobonds, 828 residues, 4 models selected > select subtract #2 Nothing selected > color #2/A:414 red > color #2/A:534 orange > color #2/A:409 green > color #2/A:409 light green > color #2/A:409 lightblue purple Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #2/A:397 purple > open /Users/sara.buscarini/Desktop/Phd/PDB/mutatedM414I/5il1M414I.pdb 5il1M414I.pdb title: Crystal structure of sam-bound METTL3-METTL14 complex [more info...] Chain information for 5il1M414I.pdb #8 --- Chain | Description | UniProt A | METTL3 | MTA70_HUMAN 369-580 B | methyltransferase-LIKE protein 14 | MET14_HUMAN 109-408 Non-standard residues in 5il1M414I.pdb #8 --- EDO — 1,2-ethanediol (ethylene glycol) SAM — S-adenosylmethionine > hide #7.1 models > hide #!7 models > hide #!2 models > color #8/A #f27a93ff > color #8/B #fcbe7cff > color #8/A:SAM green > select #8/A:SAM 27 atoms, 29 bonds, 1 residue, 1 model selected > color sel byhetero > select add #8 4336 atoms, 4102 bonds, 1 pseudobond, 828 residues, 2 models selected > select subtract #8 Nothing selected > select #8/A:414 8 atoms, 7 bonds, 1 residue, 1 model selected > style sel stick Changed 8 atom styles > show sel atoms > color #8/A:414 red > select #8/A:414 8 atoms, 7 bonds, 1 residue, 1 model selected > swapaa I #414:A No amino acid residues specified for swapping > swapaa I414M Missing or invalid ""residues"" argument: invalid residues specifier > swapaa #8/A:414 Missing or invalid ""resTypes"" argument: Expected a text string > swapaa I @414:A No amino acid residues specified for swapping > swapaa #8/A:414 ile Using Dunbrack library 5il1M414I.pdb #8/A MET 414: phi -65.1, psi -50.0 trans Applying ILE rotamer (chi angles: -62.6 -60.5) to 5il1M414I.pdb #8/A ILE 414 > save /Users/sara.buscarini/Desktop/5il1M414I.pdb > hide #!8 models > show #!8 models > save /Users/sara.buscarini/Desktop/5IL1mut.pdb No model chosen to save relative to > select add #8 4336 atoms, 4102 bonds, 1 pseudobond, 828 residues, 2 models selected > select subtract #8 Nothing selected > select add #8 4336 atoms, 4102 bonds, 1 pseudobond, 828 residues, 2 models selected No model chosen to save relative to > select subtract #8 Nothing selected > open /Users/sara.buscarini/Desktop/Phd/PDB/mutatedM414I/5il1mut.pdb Summary of feedback from opening /Users/sara.buscarini/Desktop/Phd/PDB/mutatedM414I/5il1mut.pdb --- warnings | Duplicate atom serial number found: 366 Duplicate atom serial number found: 367 Duplicate atom serial number found: 368 Duplicate atom serial number found: 369 Duplicate atom serial number found: 370 3 messages similar to the above omitted 5il1mut.pdb title: Crystal structure of sam-bound METTL3-METTL14 complex [more info...] Chain information for 5il1mut.pdb #9 --- Chain | Description | UniProt A | METTL3 | MTA70_HUMAN 369-580 B | methyltransferase-LIKE protein 14 | MET14_HUMAN 109-408 Non-standard residues in 5il1mut.pdb #9 --- EDO — 1,2-ethanediol (ethylene glycol) SAM — S-adenosylmethionine > hide #!9 models > select add #9 4336 atoms, 4102 bonds, 1 pseudobond, 828 residues, 2 models selected > show #!9 models > hide #!9 models > select subtract #9 Nothing selected > open /Users/sara.buscarini/Desktop/5il0-coot-0.pdb 5il0-coot-0.pdb title: Crystal structural of the METTL3-METTL14 complex for N6-adenosine methylation [more info...] Chain information for 5il0-coot-0.pdb #10 --- Chain | Description | UniProt A | METTL3 | MTA70_HUMAN 369-580 B | methyltransferase-LIKE protein 14 | MET14_HUMAN 109-408 Non-standard residues in 5il0-coot-0.pdb #10 --- BR — bromide ion EDO — 1,2-ethanediol (ethylene glycol) > hide #!8 models > select add #10 4347 atoms, 4115 bonds, 7 pseudobonds, 827 residues, 2 models selected > show sel cartoons > show sel surfaces > hide sel surfaces > select add #10 4347 atoms, 4115 bonds, 7 pseudobonds, 827 residues, 6 models selected > select subtract #10 2 models selected > select #10/A:414 8 atoms, 7 bonds, 1 residue, 1 model selected > show #!5 models > hide #!10 models > show #!5 surfaces > select add #5 3648 atoms, 3719 bonds, 5 pseudobonds, 464 residues, 4 models selected > show target m > hide #!5 models > hide #!9 models > hide #!10 models > hide #!8 models > hide #7.1 models > hide #!7 models > show #!5 models > hide #!6 models > hide #!4 models > hide #!3 models > hide #!2 models > hide #!1 models > hide sel & #!5 surfaces > select add #4 7370 atoms, 7319 bonds, 9 pseudobonds, 1130 residues, 8 models selected > select add #5 7370 atoms, 7319 bonds, 9 pseudobonds, 1130 residues, 10 models selected > select subtract #4 3648 atoms, 3719 bonds, 5 pseudobonds, 464 residues, 8 models selected > select subtract #5 8 atoms, 7 bonds, 1 residue, 4 models selected > select #5/A:414 8 atoms, 7 bonds, 1 residue, 1 model selected > color #5/A:414 f27a93ff Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #8/A #f27a93ff > color #5/A #f27a93ff > color #5/A:414 #f27a93ff > color #5/A:414 red > select #5/A:414 8 atoms, 7 bonds, 1 residue, 1 model selected > style sel stick Changed 8 atom styles > style sel stick Changed 8 atom styles > style sel stick Changed 8 atom styles > show sel cartoons > style sel stick Changed 8 atom styles > style sel ball Changed 8 atom styles > style sel sphere Changed 8 atom styles > hide sel atoms > show sel atoms > hide sel atoms > show sel atoms > hide sel atoms > show sel cartoons > style sel stick Changed 8 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > hide sel surfaces > show sel surfaces > hide sel cartoons > show sel cartoons > undo > style sel ball Changed 8 atom styles > style sel ball Changed 8 atom styles > style sel sphere Changed 8 atom styles > select #5/A:414 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel surfaces > style sel stick Changed 8 atom styles > show sel cartoons > style sel stick Changed 8 atom styles > style sel stick Changed 8 atom styles > style sel stick Changed 8 atom styles > select #5/A:416 11 atoms, 10 bonds, 1 residue, 1 model selected > style sel stick Changed 11 atom styles > style sel stick Changed 11 atom styles > color sel byhetero > show sel cartoons > style sel stick Changed 11 atom styles > style sel sphere Changed 11 atom styles > hide sel atoms > show sel atoms > hide sel atoms > hide sel cartoons > show sel cartoons > hide sel surfaces > show sel surfaces > hide sel surfaces > style sel stick Changed 11 atom styles > show (#!5 & sel) target ab > undo > select #5/A:414 8 atoms, 7 bonds, 1 residue, 1 model selected > show (#!5 & sel) target ab > color sel byhetero > select #5/A:398 14 atoms, 15 bonds, 1 residue, 1 model selected > show (#!5 & sel) target ab > color sel byhetero > color #5/A:398 light blue > color sel byhetero > color #5/A:398 blue > color sel byhetero > color #5/A:396 pink > select #5/A:396 pink Expected a keyword > select #5/A:396 7 atoms, 7 bonds, 1 residue, 1 model selected > show (#!5 & sel) target ab > color sel byhetero > select #5/A:378 8 atoms, 7 bonds, 1 residue, 1 model selected > color #5/A:378 purple > color sel byhetero > select #5/A:378 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel byhetero > select #5/A:377ù Expected an objects specifier or a keyword > select #5/A:377 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/A:378 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel byhetero > hide #10.3 models > hide #10.2 models > hide #10.1 models > close #9 > close #10 > close #8 > select add #5 3640 atoms, 3712 bonds, 5 pseudobonds, 463 residues, 5 models selected > select subtract #5 2 models selected > open /Users/sara.buscarini/Desktop/mutated_proteins/7o2i-coot-0.pdb 7o2i-coot-0.pdb title: METTL3-METTL14 heterodimer bound to the sam competitive small molecule inhibitor STM2457 [more info...] Chain information for 7o2i-coot-0.pdb #8 --- Chain | Description | UniProt A | N6-adenosine-methyltransferase catalytic subunit | MTA70_HUMAN 354-580 B | N6-adenosine-methyltransferase non-catalytic subunit | MET14_HUMAN 107-395 Non-standard residues in 7o2i-coot-0.pdb #8 --- DMS — dimethyl sulfoxide V22 — ~{N}-[[6-[(cyclohexylmethylamino)methyl]imidazo[1,2-A]pyridin-2-yl]methyl]-4-oxidanylidene-1~{H}-pyrido[1,2-A]pyrimidine-2-carboxamide > hide #!5 models > color #8/A #f27a93ff > color #8/B #fcbe7cff > color #8/A:V22 green > select #8/A:V22 33 atoms, 37 bonds, 1 residue, 1 model selected > color #8/A:414 red > select #8/A:414 8 atoms, 7 bonds, 1 residue, 1 model selected > swapaa #8/A:414 ileA Using Dunbrack library 7o2i-coot-0.pdb #8/A ILE 414: phi -70.9, psi -57.3 trans Dunbrack rotamer library does not support ILEA > preset ""initial styles"" sticks Using preset: Initial Styles / Sticks Preset implemented in Python; no expansion to individual ChimeraX commands available. > close #8 > preset ""initial styles"" ""original look"" Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. > color #5/A #f27a93ff > color #5/B #fcbe7cff > color #5/A:V22 green > select #5/A:V22 33 atoms, 37 bonds, 1 residue, 1 model selected > color #5/A:414 red > select #5/A:414 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/A:V22 33 atoms, 37 bonds, 1 residue, 1 model selected > color sel byhetero > select #5/A:414 8 atoms, 7 bonds, 1 residue, 1 model selected > style sel stick Changed 8 atom styles > style sel stick Changed 8 atom styles > show (#!5 & sel) target ab > color #5/A #f27a93ff > color #5/B #fcbe7cff > color #5/A:V22 green > select #5/A:V22 33 atoms, 37 bonds, 1 residue, 1 model selected > color #5/A:414 red > select #5/A:414 8 atoms, 7 bonds, 1 residue, 1 model selected > color #5/A:398 blue > select #5/A:398 14 atoms, 15 bonds, 1 residue, 1 model selected > style sel stick Changed 14 atom styles > select #5/A:396 light pink Expected a keyword > select #5/A:396 7 atoms, 7 bonds, 1 residue, 1 model selected > style sel stick Changed 7 atom styles > select #5/A:378 purple Expected a keyword > select #5/A:378 8 atoms, 7 bonds, 1 residue, 1 model selected > style sel stick Changed 8 atom styles > color #5/A #f27a93ff > color #5/B #fcbe7cff > color #5/A:V22 green > select #5/A:V22 33 atoms, 37 bonds, 1 residue, 1 model selected > color #5/A:414 red > select #5/A:414 8 atoms, 7 bonds, 1 residue, 1 model selected > color #5/A:398 blue > select #5/A:398 14 atoms, 15 bonds, 1 residue, 1 model selected > style sel stick Changed 14 atom styles > Color #5/A:396 light pink Unknown command: Color #5/A:396 light pink > select #5/A:396 7 atoms, 7 bonds, 1 residue, 1 model selected > style sel stick Changed 7 atom styles > Color #5/A:378 purple Unknown command: Color #5/A:378 purple > select #5/A:378 8 atoms, 7 bonds, 1 residue, 1 model selected > style sel stick Changed 8 atom styles > color #5/A #f27a93ff > color #5/B #fcbe7cff > color #5/A:V22 green > select #5/A:V22 33 atoms, 37 bonds, 1 residue, 1 model selected > color #5/A:414 red > select #5/A:414 8 atoms, 7 bonds, 1 residue, 1 model selected > color #5/A:398 blue > select #5/A:398 14 atoms, 15 bonds, 1 residue, 1 model selected > style sel stick Changed 14 atom styles > color #5/A:396 light pink > select #5/A:396 7 atoms, 7 bonds, 1 residue, 1 model selected > style sel stick Changed 7 atom styles > color #5/A:378 purple > select #5/A:378 8 atoms, 7 bonds, 1 residue, 1 model selected > style sel stick Changed 8 atom styles > show (#!5 & sel) target ab > select add #5 3640 atoms, 3712 bonds, 5 pseudobonds, 463 residues, 3 models selected > select subtract #5 2 models selected > select #5/A:V22 33 atoms, 37 bonds, 1 residue, 1 model selected > color sel byhetero > select add #5 3640 atoms, 3712 bonds, 5 pseudobonds, 463 residues, 2 models selected > select subtract #5 2 models selected > select #5/A:378 8 atoms, 7 bonds, 1 residue, 1 model selected > style sel stick Changed 8 atom styles > select #5/A:396 7 atoms, 7 bonds, 1 residue, 1 model selected > show (#!5 & sel) target ab > select #5/A:398 14 atoms, 15 bonds, 1 residue, 1 model selected > show (#!5 & sel) target ab > select add #5 3640 atoms, 3712 bonds, 5 pseudobonds, 463 residues, 3 models selected > select subtract #5 2 models selected > view name glutamate_role > view_nameV22 Unknown command: view_nameV22 > view_name Unknown command: view_name > view name V22 > save /Users/sara.buscarini/Desktop/1.png width 987 height 646 supersample 3 > transparentBackground true > open /Users/sara.buscarini/Desktop/mutated_proteins/7o2i-coot-0.pdb 7o2i-coot-0.pdb title: METTL3-METTL14 heterodimer bound to the sam competitive small molecule inhibitor STM2457 [more info...] Chain information for 7o2i-coot-0.pdb #8 --- Chain | Description | UniProt A | N6-adenosine-methyltransferase catalytic subunit | MTA70_HUMAN 354-580 B | N6-adenosine-methyltransferase non-catalytic subunit | MET14_HUMAN 107-395 Non-standard residues in 7o2i-coot-0.pdb #8 --- DMS — dimethyl sulfoxide V22 — ~{N}-[[6-[(cyclohexylmethylamino)methyl]imidazo[1,2-A]pyridin-2-yl]methyl]-4-oxidanylidene-1~{H}-pyrido[1,2-A]pyrimidine-2-carboxamide > hide #!5 models > color #8/A #f27a93ff > color #8/B #fcbe7cff > color #8/A:V22 green > select #8/A:V22 33 atoms, 37 bonds, 1 residue, 1 model selected > color #8/A:414 red > select #8/A:414 8 atoms, 7 bonds, 1 residue, 1 model selected > color #8/A:398 blue > select #8/A:398 14 atoms, 15 bonds, 1 residue, 1 model selected > style set stick Expected a keyword > color #8/A:396 light pink > select #5/A:396 7 atoms, 7 bonds, 1 residue, 1 model selected > show (#!5 & sel) target ab > color #8/A:378 purple > select #8/A:378 8 atoms, 7 bonds, 1 residue, 1 model selected > style sel stick Changed 8 atom styles > select #8/A:V22 33 atoms, 37 bonds, 1 residue, 1 model selected > style sel stick Changed 33 atom styles > select #8/A:V22 33 atoms, 37 bonds, 1 residue, 1 model selected > color sel byhetero > select add #8 3640 atoms, 3709 bonds, 33 pseudobonds, 463 residues, 2 models selected > select subtract #8 Nothing selected > select #8/A:443 6 atoms, 5 bonds, 1 residue, 1 model selected > color #8/A:443 water green Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #8/A:443 light green > color #8/A #f27a93ff > color #8/B #fcbe7cff > color #8/A:V22 green > select #8/A:V22 33 atoms, 37 bonds, 1 residue, 1 model selected > color #8/A:414 red > select #8/A:414 8 atoms, 7 bonds, 1 residue, 1 model selected > color #8/A:398 blue > select #8/A:398 14 atoms, 15 bonds, 1 residue, 1 model selected > show (#!5 & sel) target ab > color #8/A:396 light pink > select #5/A:396 7 atoms, 7 bonds, 1 residue, 1 model selected > show (#!5 & sel) target ab > color #8/A:378 purple > select #8/A:378 8 atoms, 7 bonds, 1 residue, 1 model selected > show (#!5 & sel) target ab > select #8/A:V22 33 atoms, 37 bonds, 1 residue, 1 model selected > show (#!5 & sel) target ab > select #8/A:V22 33 atoms, 37 bonds, 1 residue, 1 model selected > color sel byhetero > select #8/A:443 6 atoms, 5 bonds, 1 residue, 1 model selected > color #8/A:443 water green Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #8/A #f27a93ff > color #8/B #fcbe7cff > color #8/A:V22 green > select #8/A:V22 33 atoms, 37 bonds, 1 residue, 1 model selected > color #8/A:414 red > select #8/A:414 8 atoms, 7 bonds, 1 residue, 1 model selected > color #8/A:398 blue > select #8/A:398 14 atoms, 15 bonds, 1 residue, 1 model selected > show (#!5 & sel) target ab > color #8/A:396 light pink > select #5/A:396 7 atoms, 7 bonds, 1 residue, 1 model selected > show (#!5 & sel) target ab > color #8/A:378 purple > select #8/A:378 8 atoms, 7 bonds, 1 residue, 1 model selected > show (#!5 & sel) target ab > select #8/A:V22 33 atoms, 37 bonds, 1 residue, 1 model selected > show (#!5 & sel) target ab > select #8/A:V22 33 atoms, 37 bonds, 1 residue, 1 model selected > color sel byhetero > select #8/A:414 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel target ab > select #8/A:398 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel target ab > select #8/A:396 7 atoms, 7 bonds, 1 residue, 1 model selected > show sel target ab > select add #8 3640 atoms, 3709 bonds, 33 pseudobonds, 463 residues, 2 models selected > select subtract #8 Nothing selected > select #8/A:443 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel target ab > color #8/A:414 light blue > undo > color #8/A:443 light blue > select add #8 3640 atoms, 3709 bonds, 33 pseudobonds, 463 residues, 2 models selected > select subtract #8 Nothing selected > save /Users/sara.buscarini/Desktop/2.png width 987 height 619 supersample 3 > transparentBackground true > show #!5 models > show #!4 models > hide #!4 models > hide #!8 models > show #!8 models > hide #!5 models > show #!5 models > hide #!8 models > color #8/A:396 yellow > color #5/A:396 yellow > view name glutamate_role > save /Users/sara.buscarini/Desktop/7o2i_new.png width 1437 height 903 > supersample 3 transparentBackground true > save /Users/sara.buscarini/Desktop/1.png width 1437 height 903 supersample 3 > transparentBackground true > show #!8 models > hide #!5 models > select add #8 3640 atoms, 3709 bonds, 33 pseudobonds, 463 residues, 2 models selected > show #!8 target m > show sel surfaces > hide sel surfaces > select add #8 3640 atoms, 3709 bonds, 33 pseudobonds, 463 residues, 5 models selected > select subtract #8 2 models selected > save /Users/sara.buscarini/Desktop/7o2i_M414I.png width 1437 height 903 > supersample 3 transparentBackground true > show #!5 models > hide #!8 models > save /Users/sara.buscarini/Desktop/mut.png width 1437 height 903 supersample > 3 transparentBackground true > show #!8 models > hide #!5 models > view #8 clip false > select #8/A:443 6 atoms, 5 bonds, 1 residue, 1 model selected > ui tool show Distances > select #8/A:443@SG 1 atom, 1 residue, 1 model selected > select #8/A:414@CG2 1 atom, 1 residue, 1 model selected > select add #8/A:443@SG 2 atoms, 2 residues, 2 models selected > distance #8/A:414@CG2 #8/A:443@SG Distance between 7o2i-coot-0.pdb #8/A ILE 414 CG2 and CYS 443 SG: 2.954Å > distance #8/A:414@CG2 #8/A:443@SG Distance already exists; modify distance properties with 'distance style' > distance #8/A:414@CG2 #8/A:443@SG Distance already exists; modify distance properties with 'distance style' > show #!7 models > show #7.1 models > show #!5 models > hide #!7 models > hide #7.1 models > show #7.1 models > hide #!7 models > show #!7 models > hide #!7 models > hide #7.1 models > hide #!8 models > select add #8 3640 atoms, 3709 bonds, 34 pseudobonds, 463 residues, 4 models selected > select #8/A:443 6 atoms, 5 bonds, 1 residue, 1 model selected > select #5/A:443 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel target ab > olor #5/A:443 light blue Unknown command: olor #5/A:443 light blue > color #5/A:443 light blue > select #5/A:414@CE 1 atom, 1 residue, 1 model selected > select add #5/A:443@SG 2 atoms, 2 residues, 2 models selected > distance #5/A:414@CE #5/A:443@SG Distance between 7o2i.pdb #5/A MET 414 CE and CYS 443 SG: 5.168Å > show #7.1 models Unsupported scale factor (0.000000) detected on Display0 > show #!8 models > hide #7.1 models > hide #!7 models > hide #!5 models > show #7.1 models > hide #!7 models > show #!7 models > show #!5 models > hide #!7 models > hide #7.1 models > hide #!8 models Unsupported scale factor (0.000000) detected on Display0 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. Unsupported scale factor (0.000000) detected on Display0 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > view #7 clip false No displayed objects specified. > view #7 clip false No displayed objects specified. > show #!8 models > view #8 clip false > hide #!5 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > show #7.1 models > show #!5 models > hide #!7 models > show #!7 models > hide #!8 models > hide #7.1 models > hide #!7 models > show #!7 models > show #7.1 models ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M3 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: Mac15,12 Model Number: Z1B8001FCT/A Chip: Apple M3 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 10151.140.19 OS Loader Version: 10151.140.19 Software: System Software Overview: System Version: macOS 14.6 (23G80) Kernel Version: Darwin 23.6.0 Time since boot: 7 days, 20 hours, 29 minutes Graphics/Displays: Apple M3: Chipset Model: Apple M3 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: T27p-30: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 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: 2.2.4 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 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: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 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-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 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: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 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: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 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 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 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: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Window Toolkit duplicate all ChimeraX