id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14407 Crash in garbage collection while parsing atom spec chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.0-x86_64-i386-64bit ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x0000000319d63000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x0000000205288240 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/ast.py"", line 52 in File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/ast.py"", line 52 in iteritems File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/ast.py"", line 55 in items File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/ast.py"", line 92 in copy File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 642 in _try File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py"", line 137 in __enter__ File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 679 in _choice File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py"", line 137 in __enter__ File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 276 in _model_spec_start_ File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 245 in _model_range_ File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 228 in _model_range_list_ File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 213 in _model_hierarchy_ File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 177 in _model_ File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 157 in block0 File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 787 in _positive_closure File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 159 in _model_list_ File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 136 in _as_term_ File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 89 in _atom_specifier_ File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 206 in parse File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 192 in _parse_unquoted File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 121 in parse File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/args.py"", line 81 in parse File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 901 in parse File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2499 in _parse_arg File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2640 in _process_positional_arguments File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2864 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py"", line 319 in execute File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py"", line 146 in keyPressEvent File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 918 in init File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, 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, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.mmcif.mmcif_write (total: 53) {""app_name"":""ChimeraX"",""timestamp"":""2024-01-18 15:48:56.00 -0800"",""app_version"":""1.7.0"",""slice_uuid"":""194a3167-3db5-3029-8d22-1d742b826bb9"",""build_version"":""1.7.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 14.0 (23A344)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""BE760651-F0AE-4BB4-BACA-B9376E080D5A""} { ""uptime"" : 13000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""Mac14,2"", ""coalitionID"" : 1859, ""osVersion"" : { ""train"" : ""macOS 14.0"", ""build"" : ""23A344"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2024-01-18 15:48:53.0085 -0800"", ""codeSigningMonitor"" : 1, ""incident"" : ""BE760651-F0AE-4BB4-BACA-B9376E080D5A"", ""pid"" : 4241, ""translated"" : true, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2024-01-18 15:16:43.4239 -0800"", ""procStartAbsTime"" : 266495269194, 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Bytes before following region: 140722823462743\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffc95e78000-7ffcbb598000 [599.1M] r-x\/r-x SM=COW ...t_id=b581fab3"", ""exception"" : {""codes"":""0x0000000000000001, 0x00000000000000a9"",""rawCodes"":[1,169],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x00000000000000a9""}, ""termination"" : {""flags"":0,""code"":11,""namespace"":""SIGNAL"",""indicator"":""Segmentation fault: 11"",""byProc"":""ChimeraX"",""byPid"":4241}, ""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"" : ""0xa9 is not in any region. 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""\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation"", ""name"" : ""Foundation"", ""CFBundleVersion"" : ""2048.1.403"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 140703150407680, ""CFBundleShortVersionString"" : ""6.9"", ""CFBundleIdentifier"" : ""com.apple.CoreFoundation"", ""size"" : 4820989, ""uuid"" : ""c71c408a-6a88-3cd0-aebf-9012bc196571"", ""path"" : ""\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation"", ""name"" : ""CoreFoundation"", ""CFBundleVersion"" : ""2048.1.403"" } ], ""sharedCache"" : { ""base"" : 140703145590784, ""size"" : 21474836480, ""uuid"" : ""fb8ba21b-013a-3f11-b51e-5d5b4271240d"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%)\nWritable regions: Total=8.0G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=8.0G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG image 200K 19 \nColorSync 240K 30 \nCoreAnimation 748K 121 \nCoreGraphics 24K 4 \nCoreUI image data 4088K 32 \nFoundation 36K 2 \nKernel Alloc Once 8K 1 \nMALLOC 7.1G 160 \nMALLOC guard page 384K 24 \nMach message 16K 4 \nOpenGL GLSL 384K 4 \nRosetta Arena 4096K 2 \nRosetta Generic 1668K 414 \nRosetta IndirectBranch 2048K 1 \nRosetta JIT 128.0M 1 \nRosetta Return Stack 776K 76 \nRosetta Thread Context 760K 76 \nSTACK GUARD 36K 9 \nStack 177.1M 38 \nStack Guard 56.1M 29 \nVM_ALLOCATE 209.9M 337 \nVM_ALLOCATE (reserved) 160.1M 12 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 56.0M 820 \n__DATA_CONST 48.1M 447 \n__DATA_DIRTY 1862K 236 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 169.3M 152 \n__OBJC_RO 70.5M 1 \n__OBJC_RW 2151K 2 \n__TEXT 1.0G 827 \ndyld private memory 420K 4 \nmapped file 7.2G 1526 \nshared memory 3004K 22 \nunshared pmap 15.0M 9 \n=========== ======= ======= \nTOTAL 16.5G 5448 \nTOTAL, minus reserved VM space 16.3G 5448 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""4de6f12967221c24f89d22b8dfa2937e4feabcdf"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""60356660bbe37970735c5624"", ""factorPackIds"" : { }, ""deploymentId"" : 240000027 }, { ""rolloutId"" : ""64b21a7351cbb02ce3442e4e"", ""factorPackIds"" : { ""REMINDERS_GROCERY"" : ""64fbafa16ec4a304c6ba89f9"" }, ""deploymentId"" : 240000032 } ], ""experiments"" : [ ] }, ""reportNotes"" : [ ""PC register does not match crashing frame (0x0 vs 0x7FF89181AA78)"" ] } ===== Log before crash start ===== UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/yiyingli/Library/CloudStorage/OneDrive- > UCSanDiego/FtsH_1D/CryoEM_1D/TO SAVE DATA > W3/cryosparc_P3_J171_006_volume_map_sym_sharp.mrc"" format mrc Opened cryosparc_P3_J171_006_volume_map_sym_sharp.mrc as #1, grid size 448,448,448, pixel 0.86, shown at level 0.894, step 2, values float32 > open /Users/yiyingli/Library/CloudStorage/OneDrive- > UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/FtsH_fresh_group1_BiologicalAssembly.cif Summary of feedback from opening /Users/yiyingli/Library/CloudStorage/OneDrive- UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/FtsH_fresh_group1_BiologicalAssembly.cif --- warning | No mmCIF models found. > open /Users/yiyingli/Library/CloudStorage/OneDrive- > UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/FtsH_fresh_group1_BiologicalAssembly.cif Summary of feedback from opening /Users/yiyingli/Library/CloudStorage/OneDrive- UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/FtsH_fresh_group1_BiologicalAssembly.cif --- warning | No mmCIF models found. > open /Users/yiyingli/Library/CloudStorage/OneDrive- > UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/FtsH_fresh_group1.cif Summary of feedback from opening /Users/yiyingli/Library/CloudStorage/OneDrive- UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/FtsH_fresh_group1.cif --- warnings | Unknown polymer entity '1' near line 61 Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for FtsH_fresh_group1.cif #2 --- Chain | Description A | No description available > select add #2 3176 atoms, 3218 bonds, 406 residues, 1 model selected > close #2 > open ""/Users/yiyingli/Library/CloudStorage/OneDrive- > UCSanDiego/FtsH_1D/CryoEM_1D/CryoEM > final/ATP_C1_class1/FtsH_ATP_class1_refined.pdb"" Summary of feedback from opening /Users/yiyingli/Library/CloudStorage/OneDrive- UCSanDiego/FtsH_1D/CryoEM_1D/CryoEM final/ATP_C1_class1/FtsH_ATP_class1_refined.pdb --- warnings | Ignored bad PDB record found on line 20 Ignored bad PDB record found on line 21 GEOMETRY RESTRAINTS LIBRARY: CDL v1.2 Ignored bad PDB record found on line 22 DEVIATIONS FROM IDEAL VALUES. Ignored bad PDB record found on line 23 BOND : 0.003 0.027 3218 Ignored bad PDB record found on line 24 ANGLE : 0.551 7.969 4354 18 messages similar to the above omitted Chain information for FtsH_ATP_class1_refined.pdb #2 --- Chain | Description A | No description available > select add #2 3176 atoms, 3218 bonds, 406 residues, 1 model selected > close #2 > open ""/Users/yiyingli/Library/CloudStorage/OneDrive- > UCSanDiego/FtsH_1D/CryoEM_1D/CryoEM > final/ATP_C1_class1/helix_ATP_C1_refined.pdb"" Summary of feedback from opening /Users/yiyingli/Library/CloudStorage/OneDrive- UCSanDiego/FtsH_1D/CryoEM_1D/CryoEM final/ATP_C1_class1/helix_ATP_C1_refined.pdb --- warnings | Ignored bad PDB record found on line 20 Ignored bad PDB record found on line 21 GEOMETRY RESTRAINTS LIBRARY: CDL v1.2 Ignored bad PDB record found on line 22 DEVIATIONS FROM IDEAL VALUES. Ignored bad PDB record found on line 23 BOND : 0.007 0.097 96540 Ignored bad PDB record found on line 24 ANGLE : 0.891 19.396 130620 18 messages similar to the above omitted Chain information for helix_ATP_C1_refined.pdb #2 --- Chain | Description 1 3 5 7 A C E G I K M O Q S U W Y a c e g i k m o q s u w y | No description available > view orient > hide atoms > show cartoons > view orient > turn x -90 1 models #1 > view orient > turn x -90 1 models #2 > view orient > move y 5 1 models #2 > move z -5 1 models #2 > move y 5 1 models #2 > fitmap #2 inMap #1 Fit molecule helix_ATP_C1_refined.pdb (#2) to map cryosparc_P3_J171_006_volume_map_sym_sharp.mrc (#1) using 97320 atoms average map value = 0.3579, steps = 92 shifted from previous position = 2.86 rotated from previous position = 0.103 degrees atoms outside contour = 82925, contour level = 0.89396 Position of helix_ATP_C1_refined.pdb (#2) relative to cryosparc_P3_J171_006_volume_map_sym_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.99999842 -0.00002522 0.00177879 -0.36620967 0.00002472 0.99999996 0.00028057 -4.70584854 -0.00177880 -0.00028053 0.99999838 -0.11217952 Axis -0.15577836 0.98769470 0.01386645 Axis point -27.81900309 0.00000000 608.03636134 Rotation angle (degrees) 0.10318725 Shift along axis -4.59244966 > view orient > move y 2 1 models #2 > fitmap #2 inMap #1 Fit molecule helix_ATP_C1_refined.pdb (#2) to map cryosparc_P3_J171_006_volume_map_sym_sharp.mrc (#1) using 97320 atoms average map value = 0.3558, steps = 76 shifted from previous position = 2.04 rotated from previous position = 0.641 degrees atoms outside contour = 82605, contour level = 0.89396 Position of helix_ATP_C1_refined.pdb (#2) relative to cryosparc_P3_J171_006_volume_map_sym_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.99995635 0.00065020 -0.00932077 1.34280220 -0.00063582 0.99999860 0.00154569 -4.57588483 0.00932176 -0.00153970 0.99995537 0.04209690 Axis -0.16290479 -0.98430261 -0.06790001 Axis point -34.66049801 0.00000000 219.07481623 Rotation angle (degrees) 0.54259463 Shift along axis 4.28244807 > view orient > move z -2 1 models #2 > view orient > fitmap #2 inMap #1 Fit molecule helix_ATP_C1_refined.pdb (#2) to map cryosparc_P3_J171_006_volume_map_sym_sharp.mrc (#1) using 97320 atoms average map value = 1.775, steps = 76 shifted from previous position = 2.88 rotated from previous position = 0.559 degrees atoms outside contour = 27882, contour level = 0.89396 Position of helix_ATP_C1_refined.pdb (#2) relative to cryosparc_P3_J171_006_volume_map_sym_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.99999993 0.00026247 0.00028283 -0.14689119 -0.00026242 0.99999995 -0.00015807 0.10550173 -0.00028288 0.00015799 0.99999995 0.03686825 Axis 0.37900402 0.67836833 -0.62942224 Axis point 113.97586756 0.00000000 509.58952029 Rotation angle (degrees) 0.02389029 Shift along axis -0.00730901 > volume #1 step 1 > volume #1 level 1.5 > view orient > hide #!1 models > show #!1 models > save /Users/yiyingli/untransoformed.cif relModel #2 Not saving entity_poly_seq for non-authoritative sequences > save /Users/yiyingli/transformed.cif Not saving entity_poly_seq for non-authoritative sequences > open /Users/yiyingli/transformed.cif Summary of feedback from opening /Users/yiyingli/transformed.cif --- warnings | Unknown polymer entity '1' near line 430 Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for transformed.cif #3 --- Chain | Description 1 3 5 7 A C E G I K M O Q S U W Y a c e g i k m o q s u w y | No description available > open /Users/yiyingli/untransoformed.cif Summary of feedback from opening /Users/yiyingli/untransoformed.cif --- warnings | Unknown polymer entity '1' near line 430 Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for untransoformed.cif #4 --- Chain | Description 1 3 5 7 A C E G I K M O Q S U W Y a c e g i k m o q s u w y | No description available > hide #!3 models > hide #!4 models > show #!4 models > close #1 > open /Users/yiyingli/Library/CloudStorage/OneDrive- > UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/FtsH_fresh_group1_BiologicalAssembly.cif > format mmcif No such file/path: /Users/yiyingli/Library/CloudStorage/OneDrive- UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/FtsH_fresh_group1_BiologicalAssembly.cif > open ""/Users/yiyingli/Library/CloudStorage/OneDrive- > UCSanDiego/FtsH_1D/CryoEM_1D/TO SAVE DATA > W3/cryosparc_P3_J171_006_volume_map_sym_sharp.mrc"" format mrc Opened cryosparc_P3_J171_006_volume_map_sym_sharp.mrc as #1, grid size 448,448,448, pixel 0.86, shown at level 0.894, step 2, values float32 > hide #!2 models > hide atoms > show cartoons > close #2 > open ""/Users/yiyingli/Library/CloudStorage/OneDrive- > UCSanDiego/FtsH_1D/CryoEM_1D/CryoEM > final/ATP_C1_class1/helix_ATP_C1_refined.pdb"" format pdb Summary of feedback from opening /Users/yiyingli/Library/CloudStorage/OneDrive- UCSanDiego/FtsH_1D/CryoEM_1D/CryoEM final/ATP_C1_class1/helix_ATP_C1_refined.pdb --- warnings | Ignored bad PDB record found on line 20 Ignored bad PDB record found on line 21 GEOMETRY RESTRAINTS LIBRARY: CDL v1.2 Ignored bad PDB record found on line 22 DEVIATIONS FROM IDEAL VALUES. Ignored bad PDB record found on line 23 BOND : 0.007 0.097 96540 Ignored bad PDB record found on line 24 ANGLE : 0.891 19.396 130620 18 messages similar to the above omitted Chain information for helix_ATP_C1_refined.pdb #2 --- Chain | Description 1 3 5 7 A C E G I K M O Q S U W Y a c e g i k m o q s u w y | No description available > hide atoms > show cartoons > hide #!4 models > hide #!1 models > show #!1 models > volume #1 step 1 > volume #1 level 2 > view orient > ui tool show ""Side View"" > view > set bgColor white > hide #!1 models > close #3 > show #!1 models > close #4 > name extra #2/A,C,E,G,I > select extra 15880 atoms, 16090 bonds, 2030 residues, 1 model selected > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > name extra #2/A,C,E,G,I,w,1,3 > select extra 25408 atoms, 25744 bonds, 3248 residues, 1 model selected > hide #!1 models > name extra #2/A,C,E,G,I,w,1,3,5,7,y > select extra 34936 atoms, 35398 bonds, 4466 residues, 1 model selected > show #!1 models > view orient > select ~sel & ##selected 62384 atoms, 61142 bonds, 9754 residues, 1 model selected > combine sel modelId 3 > hide #!2 models > hide #!1 models > show #!1 models > select #3/A,C,E,G,I,w,1,3,5,7,y 34936 atoms, 35398 bonds, 4466 residues, 1 model selected > delete sel > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > view orient > save /Users/yiyingli/fresh_group1_assembly.cif models #3 relModel #1 Not saving entity_poly_seq for non-authoritative sequences > open /Users/yiyingli/fresh_group1_assembly.cif Summary of feedback from opening /Users/yiyingli/fresh_group1_assembly.cif --- warnings | Unknown polymer entity '1' near line 342 Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for fresh_group1_assembly.cif #4 --- Chain | Description K M O Q S U W Y a c e g i k m o q s u | No description available > hide atoms > show cartoons > hide #!3 models > volume #1 level 1 > volume #1 level 2 > view orient > close #3 > close #2 > renumber #4/W start 1 relative true 406 residues renumbered > hide #!1 models > hide #4.1 models > undo > ui tool show ""Show Sequence Viewer"" > sequence chain /K /M /O /Q /S /U /W /Y /a /c /e /g /i /k /m /o /q /s /u Alignment identifier is 1 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 86 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: Mac Model Identifier: Mac14,2 Model Number: FLY13LL/A Chip: Unknown Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 10151.1.1 OS Loader Version: 10151.1.1 Software: System Software Overview: System Version: macOS 14.0 (23A344) Kernel Version: Darwin 23.0.0 Time since boot: 20 hours, 30 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL U2414H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 50.00Hz Mirror: Off Online: Yes Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 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: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 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: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.13 ChimeraX-ModelPanel: 1.4 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: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.3 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 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-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 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: 1.33.2 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 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: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.0 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.0 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.5.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.8 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 Pillow: 10.0.1 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.3 urllib3: 2.1.0 wcwidth: 0.2.12 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Core can't reproduce Tom Goddard all ChimeraX