id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20164 ChimeraX bug report submission chimerax-bug-report@… "{{{ The following bug report has been submitted: Platform: macOS-15.3.1-arm64-arm-64bit ChimeraX Version: 1.12.dev202603310021 (2026-03-31 00:21:10 UTC) Description Last time you used ChimeraX it crashed. 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memory 992K 19 =========== ======= ======= TOTAL 8.5G 5850 TOTAL, minus reserved VM space 8.3G 5850 "", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""18acce8a9b0c47e72584c5e7a6255581c667b009"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""648cada15dbc71671bb3aa1b"", ""factorPackIds"" : { ""SIRI_EXPERIENCE_CAM"" : ""65a81173096f6a1f1ba46525"" }, ""deploymentId"" : 240000116 }, { ""rolloutId"" : ""5f72dc58705eff005a46b3a9"", ""factorPackIds"" : { }, ""deploymentId"" : 240000015 } ], ""experiments"" : [ ] } } Log: UCSF ChimeraX version: 1.12.dev202603310021 (2026-03-31) © 2016-2026 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/nature/Downloads/6YDP.cif 6YDP.cif title: 55S mammalian mitochondrial ribosome with mtEFG1 and P site fMet-tRNAMet (POST) [more info...] Chain information for 6YDP.cif #1 --- Chain | Description | UniProt AA BA | 12S rRNA | AB | Mitochondrial ribosomal protein S2 | F1S001_PIG 1-289 AC | Mitochondrial ribosomal protein S24 | A0A287ANU4_PIG 1-167 AE | Mitochondrial ribosomal protein S5 | F1SU66_PIG 1-430 AF | bS6m | I3LEJ9_PIG -151-124 AG | Mitochondrial ribosomal protein S7 | A0A286ZJ25_PIG 1-242 AI | uS9m | I3LU08_PIG 1-397 AJ | Mitochondrial ribosomal protein S10 | F1RUU2_PIG 2-201 AK | uS11m | A0A286ZJJ6_PIG 1-196 AL | Mitochondrial ribosomal protein S12 | A0A0M3KL52_PIG 1-139 AN | Mitochondrial ribosomal protein S14 | A0A0M3KL53_PIG 1-128 AO | uS15m | A0A287BMP0_PIG 1-239 AP | 28S ribosomal protein S16, mitochondrial | A0A480JTD7_PIG 1-135 AQ | uS17m | F1RIU0_PIG 1-130 AR | Mitochondrial ribosomal protein S18C | A0A0M3KL54_PIG 1-143 AU | bS21m | A0A286ZNB3_PIG 1-87 AV | fMet-tRNAMet (P site) | AX | mRNA | AZ | unknown peptide | Aa | Mitochondrial ribosomal protein S22 | A0A287AQT5_PIG 1-382 Ab | mS23 | A0A287AEW3_PIG 1-190 Ac | Mitochondrial ribosomal protein S25 | A0A0M3KL55_PIG 1-173 Ad | Mitochondrial ribosomal protein S26 | A0A287AY01_PIG 1-205 Ae | Mitochondrial ribosomal protein S27 | I3LK09_PIG 41-455 Af | Mitoribosomal protein ms28, mrps28 | A0A0M3KL56_PIG 1-188 Ag | Death associated protein 3 | I3LS10_PIG -12-397 Ah | Mitochondrial ribosomal protein S31 | F1RME2_PIG 1-387 Ai | mS33 | F1S8G3_PIG 1-106 Aj | mS34 | A0A287AVS9_PIG 1-218 Ak | Mitochondrial ribosomal protein S35 | F1SG95_PIG 1-325 Am | mS37 | F1SU49_PIG 1-118 An | Aurora kinase A interacting protein 1 | A0A287B3R8_PIG 1-199 Ao | Pentatricopeptide repeat domain 3 | K7GKS8_PIG 1-692 Ap | 28S ribosomal protein S18b, mitochondrial | RT18B_PIG 1-258 B0 | Mitochondrial ribosomal protein L27 | F1RT79_PIG 1-148 B1 | Mitochondrial ribosomal protein L28 | A0A286ZTW8_PIG 1-256 B2 | Mitochondrial ribosomal protein L47 | F1SGC7_PIG 1-252 B3 | uL30m | F1STE5_PIG 1-161 B4 | bL31m | I3L9J0_PIG 1-126 B5 | bL32m | I3LTC4_PIG 1-188 B6 | bL33m | A0A286ZU68_PIG 1-65 B7 | Mitochondrial ribosomal protein L34 | A0A287A119_PIG 1-95 B8 | Mitochondrial ribosomal protein L35 | F1SVC5_PIG 1-188 B9 | Ribosomal protein | A0A287A731_PIG 1-100 BB | CP tRNAPhe | BC | Elongation factor G, mitochondrial | EFGM_HUMAN 37-751 BD | uL2m | F1RRN2_PIG 1-306 BE | ICT1 | A0A140UHW4_PIG 1-348 BF | Mitochondrial ribosomal protein L4 | A0A287B9C4_PIG 1-294 BI | Mitochondrial ribosomal protein L9 | I3LR45_PIG 1-268 BJ | Mitochondrial ribosomal protein L10 | F1RWJ0_PIG 1-262 BK | Mitochondrial ribosomal protein L11 | F1RU54_PIG 1-192 BN | uL13m | K7GP19_PIG 1-178 BO | uL14m | A0A287BMZ6_PIG 1-145 BP | uL15m | F1RSH0_PIG 1-296 BQ | uL16m | F1RI89_PIG 1-251 BR | Uncharacterized protein | F1RMQ4_PIG 1-169 BS | Mitochondrial ribosomal protein L18 | A0A286ZNK1_PIG 1-180 BT | Mitochondrial ribosomal protein L19 | I3LNJ0_PIG 1-292 BU | Mitochondrial ribosomal protein L20 | A0A286ZU56_PIG 1-149 BV | Mitochondrial ribosomal protein L21 | F1RY70_PIG 1-209 BW | uL22m | F1RQC9_PIG 1-210 BX | uL23m | A0A286ZZC6_PIG 1-150 BY | uL24m | F1RHJ1_PIG 1-216 Ba | Mitochondrial ribosomal protein L37 | A0A287BIV6_PIG 1-423 Bb | Mitochondrial ribosomal protein L38 | F1RW03_PIG 1-380 Bc | Mitochondrial ribosomal protein L39 | F1SHP6_PIG 1-334 Bd | Uncharacterized protein | A0A286ZP98_PIG -43-162 Be | Mitochondrial ribosomal protein L41 | A0A287AWS0_PIG 1-135 Bf | mL42 | A0A287BQA1_PIG 1-142 Bg | Mitochondrial ribosomal protein L43 | F1S8U4_PIG 1-159 Bh | mL44 | F1SR64_PIG 1-332 Bi | Mitochondrial ribosomal protein L45 | I3LGM5_PIG 1-306 Bj | Mitochondrial ribosomal protein L46 | F1SRT0_PIG 1-279 Bk | 39S ribosomal protein L48, mitochondrial | A0A480J9Z6_PIG -56-212 Bl | Mrpl34 | A0A0R4J8D6_PIG 1-166 Bm | Mitochondrial ribosomal protein L50 | I3L9H6_PIG -38-159 Bn | Mitochondrial ribosomal protein L51 | A0A287BE26_PIG 1-128 Bo | mL52 | F1S9B7_PIG 1-124 Bp | mL53 | Bq | mL54 | I3LN63_PIG 1-138 Bt | Mitochondrial ribosomal protein L57 | A0A287BP93_PIG 1-102 Bu | mL62 (ICT1) | A0A286ZJR2_PIG 1-205 Bv | mL64 | A0A286ZXA6_PIG 1-222 Bw | 39S ribosomal protein S30, mitochondrial | A0A480QIM3_PIG 1-433 Bx | Mitochondrial ribosomal protein S18A | F1RRH6_PIG 1-196 CL DL EL FL GL HL LL | Mitochondrial ribosomal protein L12 | A0A287ARV8_PIG 1-198 Non-standard residues in 6YDP.cif #1 --- 5GP — guanosine-5'-monophosphate FME — N-formylmethionine GNP — phosphoaminophosphonic acid-guanylate ester GTP — guanosine-5'-triphosphate MG — magnesium ion SPM — spermine ZN — zinc ion OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M4 OpenGL vendor: Apple Python: 3.11.9 Locale: UTF-8 Qt version: PySide6 6.10.1, Qt 6.10.1 Qt runtime version: 6.10.1 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac16,1 Model Number: MW2U3CH/A Chip: Apple M4 Total Number of Cores: 10 (4 performance and 6 efficiency) Memory: 16 GB System Firmware Version: 11881.81.4 OS Loader Version: 11881.81.4 Software: System Software Overview: System Version: macOS 15.3.1 (24D70) Kernel Version: Darwin 24.3.0 Time since boot: 18分钟24秒钟 Graphics/Displays: Apple M4: Chipset Model: Apple M4 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: accessible-pygments: 0.0.5 aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.13.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 26.1.0 babel: 2.18.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 4.1.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.6 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.2 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.66 ChimeraX-AtomicLibrary: 14.4 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4.1 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-Cluster: 1.0 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.1 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.12.dev202603310021 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.2.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.8.2 ChimeraX-Label: 1.3 ChimeraX-LightingGUI: 1.0 ChimeraX-ListInfo: 1.3.1 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.2.0 ChimeraX-MDcrds: 2.19 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.8 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.23 ChimeraX-ModelPanel: 1.6.1 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: 1.0.1 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.15.4 ChimeraX-OpenFold: 1.0 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.13 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.5.3 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.8.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.12 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.18 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SNFG: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.3 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: 2.5.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.50.3 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.6.1 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: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.3.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.5 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.2.4 debugpy: 1.8.20 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.62.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.16.0 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.11 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 2.0.0 iniconfig: 2.3.0 ipykernel: 7.1.0 ipython: 9.9.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.8 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.8.0 jupyter_core: 5.9.1 jupyterlab_widgets: 3.0.16 kiwisolver: 1.5.0 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.1 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 OpenMM: 8.4.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.6 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.9.4 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.12.5 pydantic-settings: 2.13.1 pydantic_core: 2.41.5 pydata-sphinx-theme: 0.16.1 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.5.0 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PySide6: 6.10.1 PySide6_Addons: 6.10.1 PySide6_Essentials: 6.10.1 pytest: 9.0.2 pytest-cov: 7.1.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.2 python-multipart: 0.0.22 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.1.0 rpds-py: 0.30.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 shiboken6: 6.10.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8.3 Sphinx: 9.0.4 sphinx-autodoc-typehints: 3.6.1 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 sse-starlette: 3.3.4 stack-data: 0.6.3 starlette: 1.0.0 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.5 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 urllib3: 2.6.3 uvicorn: 0.42.0 wcwidth: 0.6.0 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.23.0 }}} " defect new normal Unassigned