id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15268 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.4.1-x86_64-i386-64bit ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x000070000d94c000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00007ff84d2d0100 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/ast.py"", line 63 in update File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/ast.py"", line 19 in __init__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/ast.py"", line 90 in copy File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 642 in _try File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py"", line 137 in __enter__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 665 in _option File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py"", line 137 in __enter__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 371 in _residue_ File ""/Applications/ChimeraX-1.7.1.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-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 359 in block7 File ""/Applications/ChimeraX-1.7.1.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-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 361 in _chain_ File ""/Applications/ChimeraX-1.7.1.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-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 323 in block0 File ""/Applications/ChimeraX-1.7.1.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-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 325 in _model_parts_ File ""/Applications/ChimeraX-1.7.1.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-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 200 in _model_ File ""/Applications/ChimeraX-1.7.1.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-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper File ""/Applications/ChimeraX-1.7.1.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-1.7.1.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-1.7.1.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-1.7.1.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-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper File ""/Applications/ChimeraX-1.7.1.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-1.7.1.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-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper File ""/Applications/ChimeraX-1.7.1.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-1.7.1.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-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 93 in _atom_specifier_ File ""/Applications/ChimeraX-1.7.1.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-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 206 in parse File ""/Applications/ChimeraX-1.7.1.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-1.7.1.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-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/defattr.py"", line 180 in defattr File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/add_charge/charge.py"", line 81 in add_standard_charges File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/add_charge/charge.py"", line 34 in add_charges File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/coulombic.py"", line 110 in assign_charges File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/cmd.py"", line 99 in cmd_coulombic File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 49 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 525 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 582 in run_expanded_command File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 72 in func_plus_tip File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 339 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 420 in run_shortcut File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 402 in try_shortcut File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 1376 in run_provider File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/__init__.py"", line 66 in run_provider File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py"", line 1302 in run_provider File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py"", line 397 in run_provider File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/toolbar/tool.py"", line 205 in callback File ""/Applications/ChimeraX-1.7.1.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-1.7.1.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-1.7.1.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.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.pdb_lib._load_libs, 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.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 59) {""app_name"":""ChimeraX"",""timestamp"":""2024-05-21 22:19:48.00 +0100"",""app_version"":""1.7.1"",""slice_uuid"":""194a3167-3db5-3029-8d22-1d742b826bb9"",""build_version"":""1.7.1.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 14.4.1 (23E224)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""86DB3C35-BEF5-4595-AB6C-018868671A69""} { ""uptime"" : 1800, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 1128307364, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro16,1"", ""coalitionID"" : 881, ""osVersion"" : { ""train"" : ""macOS 14.4.1"", ""build"" : ""23E224"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2024-05-21 22:19:39.1386 +0100"", ""codeSigningMonitor"" : 0, ""incident"" : ""86DB3C35-BEF5-4595-AB6C-018868671A69"", ""pid"" : 944, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2024-05-21 21:49:40.2839 +0100"", ""procStartAbsTime"" : 85689975144, ""procExitAbsTime"" : 1884565401495, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.7.1"",""CFBundleVersion"":""1.7.1.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""17423086-4649-5655-8652-0ADDB9D62739"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""D4945465-AD9F-9A5A-197B-8F817ADA25CA"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""bridgeVersion"" : {""build"":""21P4222"",""train"":""8.4""}, ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0xa9 is not in any region. 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All rights reserved. How to cite UCSF ChimeraX > open /Volumes/DATA/DCT/UCCT/HITDISSD/HDSD_Work/jwiebe/BCL6/240502_VMXI/VMXi- > AB2883_47x/Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb Summary of feedback from opening /Volumes/DATA/DCT/UCCT/HITDISSD/HDSD_Work/jwiebe/BCL6/240502_VMXI/VMXi- AB2883_47x/Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb --- warnings | Ignored bad PDB record found on line 2 REMARK --------------------- added by autoBUSTER ------------------------------- Ignored bad PDB record found on line 3 REMARK run at = Mon May 20 16:22:27 BST 2024 Ignored bad PDB record found on line 13 REMARK Files used: Ignored bad PDB record found on line 14 REMARK PDB = buster05/pdbchk.pdb Ignored bad PDB record found on line 15 REMARK MTZ = buster05/mtzchk.mtz 49 messages similar to the above omitted Chain information for Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #1 --- Chain | Description A | No description available > open > /Volumes/DATA/DCT/UCCT/HITDISSD/HDSD_Work/jwiebe/BCL6/231206_mx34334-7/BCL6_13/BCL6_apo- > structure.pdb Summary of feedback from opening /Volumes/DATA/DCT/UCCT/HITDISSD/HDSD_Work/jwiebe/BCL6/231206_mx34334-7/BCL6_13/BCL6_apo- structure.pdb --- warnings | Ignored bad PDB record found on line 2 REMARK --------------------- added by autoBUSTER ------------------------------- Ignored bad PDB record found on line 3 REMARK run at = Thu Jan 11 16:00:30 GMT 2024 Ignored bad PDB record found on line 12 REMARK Files used: Ignored bad PDB record found on line 13 REMARK PDB = buster11/pdbchk.pdb Ignored bad PDB record found on line 14 REMARK MTZ = /data/rds/HDSD_Work/jwiebe/BCL6/231206_mx34334-7/BCL 109 messages similar to the above omitted Chain information for BCL6_apo-structure.pdb #2 --- Chain | Description A | No description available > close > open > /Volumes/DATA/DCT/UCCT/HITDISSD/HDSD_Work/jwiebe/BCL6/231206_mx34334-7/BCL6_13/BCL6_apo- > structure.pdb format pdb Summary of feedback from opening /Volumes/DATA/DCT/UCCT/HITDISSD/HDSD_Work/jwiebe/BCL6/231206_mx34334-7/BCL6_13/BCL6_apo- structure.pdb --- warnings | Ignored bad PDB record found on line 2 REMARK --------------------- added by autoBUSTER ------------------------------- Ignored bad PDB record found on line 3 REMARK run at = Thu Jan 11 16:00:30 GMT 2024 Ignored bad PDB record found on line 12 REMARK Files used: Ignored bad PDB record found on line 13 REMARK PDB = buster11/pdbchk.pdb Ignored bad PDB record found on line 14 REMARK MTZ = /data/rds/HDSD_Work/jwiebe/BCL6/231206_mx34334-7/BCL 109 messages similar to the above omitted Chain information for BCL6_apo-structure.pdb #1 --- Chain | Description A | No description available > open /Volumes/DATA/DCT/UCCT/HITDISSD/HDSD_Work/jwiebe/BCL6/240502_VMXI/VMXi- > AB2883_47x/Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb Summary of feedback from opening /Volumes/DATA/DCT/UCCT/HITDISSD/HDSD_Work/jwiebe/BCL6/240502_VMXI/VMXi- AB2883_47x/Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb --- warnings | Ignored bad PDB record found on line 2 REMARK --------------------- added by autoBUSTER ------------------------------- Ignored bad PDB record found on line 3 REMARK run at = Mon May 20 16:22:27 BST 2024 Ignored bad PDB record found on line 13 REMARK Files used: Ignored bad PDB record found on line 14 REMARK PDB = buster05/pdbchk.pdb Ignored bad PDB record found on line 15 REMARK MTZ = buster05/mtzchk.mtz 49 messages similar to the above omitted Chain information for Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2 --- Chain | Description A | No description available > ui tool show Distances > matchmaker Missing or invalid ""matchAtoms"" argument: empty atom specifier > matchmaker /A /B Missing required ""to"" argument > matchmaker #1 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb, chain A (#2) with BCL6_apo-structure.pdb, chain A (#1), sequence alignment score = 656.4 RMSD between 130 pruned atom pairs is 0.348 angstroms; (across all 131 pairs: 0.408) > hide atoms > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > select add #1 1195 atoms, 1044 bonds, 298 residues, 1 model selected > select add #2 2237 atoms, 2064 bonds, 467 residues, 2 models selected > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > ui tool show ""Color Actions"" > coulombic sel The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: BCL6_apo-structure.pdb #1/A LEU 0 BCL6_apo-structure.pdb #1/A ARG 13 BCL6_apo-structure.pdb #1/A ARG 28 BCL6_apo-structure.pdb #1/A GLN 64 BCL6_apo-structure.pdb #1/A GLU 77 BCL6_apo-structure.pdb #1/A ARG 98 BCL6_apo-structure.pdb #1/A GLU 115 BCL6_apo-structure.pdb #1/A LYS 123 BCL6_apo-structure.pdb #1/A LYS 126 BCL6_apo-structure.pdb #1/A GLU 129 Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A SER 7 Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A ILE 9 Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A ARG 13 Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A ARG 28 Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A ARG 40 Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A ARG 44 Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A GLN 64 Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A LEU 65 Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A GLU 81 Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A ARG 94 Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A ARG 98 Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A GLU 99 Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A GLU 115 Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A ARG 122 Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A LYS 123 Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A ILE 125 Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A LYS 126 Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A SER 128 Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A GLU 129 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for BCL6_apo-structure.pdb_A SES surface #1.1: minimum, -10.04, mean -0.53, maximum 9.43 Coulombic values for Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb_A SES surface #2.1: minimum, -15.18, mean -1.32, maximum 8.26 To also show corresponding color key, enter the above coulombic command and add key true > transparency /A 50 > transparency /B 50 > transparency /B 70 > transparency /A 70 > transparency /A 90 > select subtract #1 1042 atoms, 1020 bonds, 169 residues, 3 models selected > select subtract #2 1 model selected > transparency /A 70 > close #2 > close > open > /Volumes/DATA/DCT/UCCT/HITDISSD/HDSD_Work/jwiebe/BCL6/240206_mx34334-11/BCL6_CCT368763_2/BCL6_CCT368763_2_buster12.2-YV- > final.pdb format pdb Summary of feedback from opening /Volumes/DATA/DCT/UCCT/HITDISSD/HDSD_Work/jwiebe/BCL6/240206_mx34334-11/BCL6_CCT368763_2/BCL6_CCT368763_2_buster12.2-YV- final.pdb --- warnings | Ignored bad PDB record found on line 2 REMARK --------------------- added by autoBUSTER ------------------------------- Ignored bad PDB record found on line 3 REMARK run at = Wed Mar 6 15:12:54 GMT 2024 Ignored bad PDB record found on line 14 REMARK Files used: Ignored bad PDB record found on line 15 REMARK PDB = buster12.2-YV_fixed/pdbchk.pdb Ignored bad PDB record found on line 16 REMARK MTZ = /data/rds/HDSD_Work/jwiebe/BCL6/240206_mx34334-11/BC 119 messages similar to the above omitted Chain information for BCL6_CCT368763_2_buster12.2-YV-final.pdb #1 --- Chain | Description A | No description available Drag select of 2 residues > hide sel atoms > select add #1 1226 atoms, 1082 bonds, 294 residues, 1 model selected > hide sel atoms > select ::name=""763"" 19 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > select add #1 1226 atoms, 1082 bonds, 294 residues, 1 model selected > color sel light sea green > color sel light gray > color sel forest green > color sel orange > color sel orange red > color sel hot pink > ui tool show ""Color Actions"" > color sel cornflower blue > color sel light sea green > color sel cornflower blue > color sel dark red > color sel maroon > color sel crimson > color sel orange red > color sel crimson > color sel cornflower blue > select ::name=""763"" 19 atoms, 21 bonds, 1 residue, 1 model selected > color sel byhetero > ui tool show ""Crystal Contacts"" > ui tool show ""Unit Cell"" > unitcell #1 > select add #2.1 1245 atoms, 1103 bonds, 295 residues, 2 models selected > close #2.1 > select add #2.2 1245 atoms, 1103 bonds, 295 residues, 2 models selected > select add #2.8 2471 atoms, 2185 bonds, 589 residues, 3 models selected > select add #2.7 3697 atoms, 3267 bonds, 883 residues, 4 models selected > select add #2.6 4923 atoms, 4349 bonds, 1177 residues, 5 models selected > close #2.7 > select add #2.4 4923 atoms, 4349 bonds, 1177 residues, 5 models selected > select add #2.5 6149 atoms, 5431 bonds, 1471 residues, 6 models selected > select add #2.3 7375 atoms, 6513 bonds, 1765 residues, 7 models selected > close #2.3 > close #2.2 > close #2.4 > close #2.5 > close #2.11 > close #2.10 > close #2.9 > close #2.8 > close #2.6 > select add #2.12 1245 atoms, 1103 bonds, 295 residues, 2 models selected > color sel dark gray > select ::name=""763"" 38 atoms, 42 bonds, 2 residues, 2 models selected > color #1/A 763 green Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #1/A 763 201 green Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #1/A 763 201 green Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #1/A 201 green Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #1/A 201 green Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > select clear > select up Nothing selected > select #1/A:201@C3 1 atom, 1 residue, 1 model selected > select add ::name=""763"" 38 atoms, 42 bonds, 2 residues, 2 models selected > color green #1/A 201 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color /A 201 green Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel cornflower blue > color sel byhetero Drag select of 3 residues > select 2452 atoms, 2164 bonds, 588 residues, 3 models selected > select add #1/A#2.12/A 2452 atoms, 2164 bonds, 588 residues, 3 models selected > coulombic sel The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: BCL6_CCT368763_2_buster12.2-YV-final.pdb #1/A ASN -1 BCL6_CCT368763_2_buster12.2-YV-final.pdb #1/A LEU 0 BCL6_CCT368763_2_buster12.2-YV-final.pdb #1/A GLN 64 BCL6_CCT368763_2_buster12.2-YV-final.pdb #1/A ARG 98 BCL6_CCT368763_2_buster12.2-YV-final.pdb #1/A LYS 126 BCL6_CCT368763_2_buster12.2-YV-final.pdb #12 #2.12/A ASN -1 BCL6_CCT368763_2_buster12.2-YV-final.pdb #12 #2.12/A LEU 0 BCL6_CCT368763_2_buster12.2-YV-final.pdb #12 #2.12/A GLN 64 BCL6_CCT368763_2_buster12.2-YV-final.pdb #12 #2.12/A ARG 98 BCL6_CCT368763_2_buster12.2-YV-final.pdb #12 #2.12/A LYS 126 ===== Log before crash end ===== Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-5.5.17 OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine OpenGL vendor: ATI Technologies Inc. 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: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 8-Core Intel Core i9 Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.4222.0.0,0) OS Loader Version: 580~1678 Software: System Software Overview: System Version: macOS 14.4.1 (23E224) Kernel Version: Darwin 23.4.0 Time since boot: 32 minutes, 12 seconds Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0002 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 AMD Radeon Pro 5300M: Chipset Model: AMD Radeon Pro 5300M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0043 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32207P1-020 Option ROM Version: 113-D32207P1-020 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal C27F390: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: HTQJ401719 Mirror: Off Online: Yes Rotation: Supported Adapter Type: DVI or HDMI Installed Packages: alabaster: 0.7.16 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: 2.12.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.5 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-Clipper: 0.22.4 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: 1.7.1 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: 2.6.1 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: 1.5.14 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: 1.0.4 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: 1.12.4 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: 1.33.3 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: 0.2.1 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: 4.47.2 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: 5.7.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.4 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.6.0 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: 10.2.0 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: 1.0.8 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: 0.5.0 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: 2023.4 urllib3: 2.1.0 wcwidth: 0.2.13 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Core duplicate Tom Goddard all ChimeraX