id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18152 Crash in readcif::CIFFile::parse chimerax-bug-report@… Greg Couch "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.6rc202303292224 (2023-03-29 22:24:14 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x0000700014615000 (most recent call first): File ""/Applications/ChimeraX-1.6-rc2023.03.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 316 in wait File ""/Applications/ChimeraX-1.6-rc2023.03.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 574 in wait File ""/Applications/ChimeraX-1.6-rc2023.03.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 1297 in run File ""/Applications/ChimeraX-1.6-rc2023.03.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6-rc2023.03.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Current thread 0x00007ff85659bdc0 (most recent call first): File ""/Applications/ChimeraX-1.6-rc2023.03.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/mmcif/__init__.py"", line 43 in open File ""/Applications/ChimeraX-1.6-rc2023.03.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py"", line 435 in remember_data_format File ""/Applications/ChimeraX-1.6-rc2023.03.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py"", line 464 in collated_open File ""/Applications/ChimeraX-1.6-rc2023.03.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py"", line 194 in provider_open File ""/Applications/ChimeraX-1.6-rc2023.03.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py"", line 2897 in run File ""/Applications/ChimeraX-1.6-rc2023.03.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py"", line 119 in cmd_open File ""/Applications/ChimeraX-1.6-rc2023.03.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py"", line 2897 in run File ""/Applications/ChimeraX-1.6-rc2023.03.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/run.py"", line 38 in run File ""/Applications/ChimeraX-1.6-rc2023.03.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 1927 in _open_dropped_file File ""/Applications/ChimeraX-1.6-rc2023.03.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 572 in dropEvent File 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""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""f3f0648325cadd33d4227dc474469142cda2dfc1"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""67d07cd6a7affa169ae21f45"", ""factorPackIds"" : { }, ""deploymentId"" : 240000002 }, { ""rolloutId"" : ""64c17a9925d75a7281053d4c"", ""factorPackIds"" : { ""SIRI_AUDIO_DISABLE_MEDIA_ENTITY_SYNC"" : ""64d29746ad29a465b3bbeace"" }, ""deploymentId"" : 240000002 } ], ""experiments"" : [ { ""treatmentId"" : ""28060e10-d4e5-4163-aa2b-d8bd088d5cbf"", ""experimentId"" : ""6685b283afc7c17197d69eec"", ""deploymentId"" : 400000011 } ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.6rc202303292224 (2023-03-29) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/osperand/Dropbox/work/Research/ArgoBio/Evotec-lib/hit- > optimization/E191_md.pdb Summary of feedback from opening /Users/osperand/Dropbox/work/Research/ArgoBio/Evotec-lib/hit- optimization/E191_md.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK GENERATED BY TRJCONV Ignored bad PDB record found on line 3 REMARK THIS IS A SIMULATION BOX E191_md.pdb title: Title t= 5800.00000 step= 2900000 [more info...] Chain information for E191_md.pdb #1 --- Chain | Description ? | No description available Non-standard residues in E191_md.pdb #1 --- CVAL — (cval) E19 — (E19) NLEU — (nleu) > open /Users/osperand/Dropbox/work/Research/ArgoBio/Evotec-lib/hit- > optimization/Sec61-A347-draft1_alt.pdb Chain information for Sec61-A347-draft1_alt.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available > matchmaker #2, #1 Missing or invalid ""matchAtoms"" argument: only initial part ""#2"" of atom specifier valid > matchmaker #2 #1 Missing required ""to"" argument > matchmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker E191_md.pdb, chain (blank) (#1) with Sec61-A347-draft1_alt.pdb, chain A (#2), sequence alignment score = 2206.8 RMSD between 348 pruned atom pairs is 1.074 angstroms; (across all 449 pairs: 2.309) > open /Users/osperand/Dropbox/work/Research/ArgoBio/Evotec-lib/hit- > optimization/Sec61-KZR261.pdb Chain information for Sec61-KZR261.pdb #3 --- Chain | Description A | No description available B | No description available C | No description available > matchmaker #3 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker E191_md.pdb, chain (blank) (#1) with Sec61-KZR261.pdb, chain A (#3), sequence alignment score = 2167.9 RMSD between 350 pruned atom pairs is 1.062 angstroms; (across all 448 pairs: 1.785) > lighting soft > hide #!3 models > hide #!2 models > select #1/?:469@C13 1 atom, 1 residue, 1 model selected > cofr sel > select clear > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > show #!2 models > ui tool show Distances > select #2/A:501@O17 1 atom, 1 residue, 1 model selected > select #2/A:82@OG 1 atom, 1 residue, 1 model selected Exactly two atoms must be selected! > select add #2/A:501@O17 2 atoms, 2 residues, 1 model selected > distance #2/A:82@OG #2/A:501@O17 Distance between Sec61-A347-draft1_alt.pdb #2/A SER 82 OG and LIG 501 O17: 3.760Å > ~distance #2/A:82@OG #2/A:501@O17 > show #!3 models > select #3/A:501@F03 1 atom, 1 residue, 1 model selected > select #3/A:501@F03 1 atom, 1 residue, 1 model selected > select #3/A:501@F03 1 atom, 1 residue, 1 model selected > hide #!2 models > hide #1 models > show #!2 models > hide #!3 models > show #1 models > open /Users/osperand/Dropbox/work/Research/ArgoBio/Evotec-lib/hit- > optimization/A317_model_0.cif ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.6rc202303292224 (2023-03-29) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-7.0.3 OpenGL renderer: AMD Radeon Pro 5700 XT OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.9.11 Locale: en_US.UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac20,2 Processor Name: 10-Core Intel Core i9 Processor Speed: 3,6 GHz Number of Processors: 1 Total Number of Cores: 10 L2 Cache (per Core): 256 KB L3 Cache: 20 MB Hyper-Threading Technology: Enabled Memory: 32 GB System Firmware Version: 2075.120.2.0.0 (iBridge: 22.16.15072.0.0,0) OS Loader Version: 583~1350 Software: System Software Overview: System Version: macOS 15.5 (24F74) Kernel Version: Darwin 24.5.0 Time since boot: 49 jours, 21 heures et 31 minutes Graphics/Displays: AMD Radeon Pro 5700 XT: Chipset Model: AMD Radeon Pro 5700 XT Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 16 GB Vendor: AMD (0x1002) Device ID: 0x7319 Revision ID: 0x0040 ROM Revision: 113-D1820Q-231 VBIOS Version: 113-D182A2XT-013 Option ROM Version: 113-D182A2XT-013 EFI Driver Version: 01.01.231 Metal Support: Metal 3 Displays: iMac: Display Type: Built-In Retina LCD Resolution: Retina 5K (5120 x 2880) Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal LED Cinema Display: Display Type: LCD Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: W82320EY6JL Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: Yes Connection Type: Thunderbolt/DisplayPort Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9 ChimeraX-AddH: 2.2.4 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 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: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 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: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6rc202303292224 ChimeraX-CoreFormats: 1.1 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 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ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StarMap: 1.2.15 ChimeraX-StdCommands: 1.10.2 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: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.6 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 6.1.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.2.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 pyqtgraph: 0.13.7 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 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: 2.4 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.9.0 typing-extensions: 4.5.0 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Input/Output can't reproduce all ChimeraX