Opened 2 years ago
Closed 2 years ago
#10131 closed defect (fixed)
Ribbon going through RNA adduct instead of base
Reported by: | Tristan Croll | Owned by: | Tom Goddard |
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Priority: | normal | Milestone: | |
Component: | Depiction | Version: | |
Keywords: | Cc: | Greg Couch, Eric Pettersen | |
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Windows-10-10.0.22621 ChimeraX Version: 1.7.dev202311052311 (2023-11-05 23:11:54 UTC) Description Nucleic acid cartoon drawing goes wonky through the non-standard RNA base 12A - spline is going through the CA atom of a threonine adduct on the base, introducing a huge kink. Log: > isolde shorthand Initialising ISOLDE-specific command aliases: Alias Equivalent full command ------------------------------------------------- st isolde step {arguments} aw isolde add water {arguments} awsf isolde add water {arguments} sim false al isolde add ligand {arguments} aa isolde add aa $1 sel {arguments} ht isolde mod his sel {arguments} so setattr sel atoms occupancy {arguments} ab isolde adjust bfactors {arguments} ss isolde sim start sel rt isolde release torsions sel {arguments} rd isolde release distances sel {arguments} ra rd; rt pf isolde pepflip sel cf isolde cisflip sel cbb color bfactor {arguments} cbo color byattr occupancy {arguments} cbc color {arguments} bychain; color {arguments} byhet cs clipper set contourSensitivity {arguments} UCSF ChimeraX version: 1.7.dev202311052311 (2023-11-05) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 6sgc 6sgc title: Rabbit 80S ribosome stalled on a poly(A) tail [more info...] Chain information for 6sgc #1 --- Chain | Description | UniProt 23 33 | tRNA (Lys3) | 54 | 28S ribosomal RNA | 74 | 5S ribosomal RNA | 84 | 5.8S ribosomal RNA | A1 | 18S ribosomal RNA | A2 | Ribosomal protein L8 | G1TT27_RABIT 1-257 B | Ribosomal protein | G1SKZ8_RABIT 1-217 B1 | uS2 | B2 | uL3 | G1TL06_RABIT 2-403 C1 | 40S ribosomal protein S3a | G1SS70_RABIT 1-264 C2 | uL4 | D1 | uS5 | D2 | 60S ribosomal protein L5 | G1SYJ6_RABIT 2-297 E1 | uS5 | G1TNM3_RABIT 1-243 E2 | 60S ribosomal protein L6 | G1SKF7_RABIT 1-291 F1 | 40S ribosomal protein S4 | G1TK17_RABIT 1-263 F2 | uL30 | G1TUB1_RABIT 1-247 G1 | Ribosomal protein S5 | G1TFM5_RABIT 1-204 G2 | eL8 | H1 | 40S ribosomal protein S6 | G1TM55_RABIT 1-249 H2 | uL6 | G1TX33_RABIT 1-192 I1 | 40S ribosomal protein S7 | G1SVB0_RABIT 1-194 I2 | 60S ribosomal protein L10 | B7NZQ2_RABIT 1-214 J1 | 40S ribosomal protein S8 | G1TJW1_RABIT 1-208 J2 | Ribosomal protein L11 | G1TUB8_RABIT 1-178 K1 | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT 1-194 L1 | S10_plectin domain-ontaining protein | G1TPV3_RABIT 1-165 L2 | eL13 | M1 | Ribosomal protein S11 | G1TRM4_RABIT 1-158 M2 | Ribosomal protein L14 | G1SZ12_RABIT 1-218 N1 | 40S ribosomal protein S12 | G1SFR8_RABIT 1-132 N2 | Ribosomal protein L15 | G1T0C1_RABIT 1-204 O1 | Ribosomal_S13_N domain-containing protein | G1SP51_RABIT 1-151 O2 | uL13 | P1 | uS11 | P2 | uL22 | G1TVT6_RABIT 1-184 Q1 | uS19 | G1U0Q2_RABIT 1-145 Q2 | eL18 | R1 | Ribosomal protein S16 | G1SGX4_RABIT 1-146 R2 | eL19 | S1 | eS17 | G1TU13_RABIT 1-135 S2 | eL20 | T1 | eS13 | G1TPG3_RABIT 1-152 T2 | eL21 | G1SHQ2_RABIT 1-160 U1 | eS19 | G1TN62_RABIT 1-145 U2 | eL22 | V1 | Ribosomal_S10 domain-containing protein | G1SIZ2_RABIT 1-119 V2 | Ribosomal protein L23 | G1T6D1_RABIT 1-140 W1 | eS21 | W2 | TRASH domain-containing protein | G1SE28_RABIT 1-157 X1 | Ribosomal protein S15a | G1TG89_RABIT 1-130 X2 | Ribosomal_L23eN domain-containing protein | G1SE76_RABIT 1-156 XX | poly-lysine nascent chain | Y1 | uS12 | Y2 | Ribosomal protein L26 | G1SQH0_RABIT 1-145 Z1 | eS24 | Z2 | 60S ribosomal protein L27 | G1TXF6_RABIT 1-136 a1 | eS25 | G1TDB3_RABIT 1-125 a2 | Ribosomal_L18e/L15P domain-containing protein | G1SNY0_RABIT 2-148 b1 | eS26 | b2 | eL29 | c1 | 40S ribosomal protein S27 | G1TZ76_RABIT 1-84 c2 | Ribosomal_L7Ae domain-containing protein | G1TDL2_RABIT 1-115 d1 | Ribosomal protein S28 | G1TIB4_RABIT 1-69 d2 | eL31 | G1SHG0_RABIT 1-125 e1 | uS14 | G1U7M4_RABIT 1-56 e2 | eL32 | G1U437_RABIT 1-135 f1 | 40S ribosomal protein S30 | G1T8A2_RABIT 0-132 f2 | eL33 | G1SF08_RABIT 1-110 g1 | Ribosomal protein S27a | G1SK22_RABIT 1-156 g2 | eL34 | G1U945_RABIT 1-116 h1 | WD_REPEATS_REGION domain-containing protein | G1SJB4_RABIT 1-317 h2 | uL29 | G1SIT5_RABIT 1-123 i1 | polyA mRNA | i2 | 60S ribosomal protein L36 | G1TTQ5_RABIT 1-105 j2 | Ribosomal protein L37 | U3KPD5_RABIT 1-97 k2 | eL38 | G1U001_RABIT 1-70 l2 | eL39 | G1TTN1_RABIT 1-51 m2 | eL40 | n2 | 60s ribosomal protein l41 | A0A087WNH4_RABIT 1-25 o2 | eL42 | G1U344_RABIT 1-106 p2 | eL43 | G1SY53_RABIT 1-92 r2 | Ribosomal_L28e domain-containing protein | G1U7L1_RABIT 1-137 s2 | uL10 | t2 | Ribosomal protein L12 | G1SMR7_RABIT 1-165 Non-standard residues in 6sgc #1 --- MG — magnesium ion SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34)) ZN — zinc ion > cartoon > style stick Changed 218966 atom styles > color byhetero > view /23:37 OpenGL version: 3.3.0 NVIDIA 529.08 OpenGL renderer: NVIDIA GeForce RTX 3070 Laptop GPU/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.2 Locale: en_GB.cp1252 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: windows Manufacturer: HP Model: HP ZBook Studio 15.6 inch G8 Mobile Workstation PC OS: Microsoft Windows 11 Pro (Build 22621) Memory: 34,007,068,672 MaxProcessMemory: 137,438,953,344 CPU: 16 11th Gen Intel(R) Core(TM) i7-11800H @ 2.30GHz OSLanguage: en-GB Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 asttokens: 2.4.1 Babel: 2.13.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2023.7.22 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.12 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: 12.0 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: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.22.1 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.4 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.dev202311052311 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: 1.1.2 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-ISOLDE: 1.7.dev0 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.1 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: 1.5.12 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 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.2 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: 1.12.2 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: 2.2.2 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-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.3 ChimeraX-XMAS: 1.1.2 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.4 comtypes: 1.1.14 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 et-xmlfile: 1.1.0 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.44.0 funcparserlib: 1.0.1 glfw: 2.6.2 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.4 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: 5.5.0 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: 2.8.7 numpy: 1.25.1 openpyxl: 3.1.2 openvr: 1.23.701 packaging: 23.2 pandas: 2.0.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pickleshare: 0.7.5 Pillow: 10.0.1 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.11.0 prompt-toolkit: 3.0.39 psutil: 5.9.5 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 pywin32: 305 pyzmq: 25.1.1 qtconsole: 5.4.3 QtPy: 2.4.1 QtRangeSlider: 0.1.5 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 seaborn: 0.12.2 Send2Trash: 1.8.2 SEQCROW: 1.7.3 setuptools: 67.4.0 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: 6.3.3 traitlets: 5.9.0 typing-extensions: 4.8.0 tzdata: 2023.3 urllib3: 2.0.7 wcwidth: 0.2.9 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 WMI: 1.5.1
Change History (3)
comment:1 by , 2 years ago
Platform: | → all |
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Project: | → ChimeraX |
comment:2 by , 2 years ago
Cc: | added |
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Component: | Unassigned → Depiction |
Owner: | set to |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → Ribbon going through RNA adduct instead of base |
comment:3 by , 2 years ago
Resolution: | → fixed |
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Status: | assigned → closed |
Fixed in daily build and 1.7 release candidate.
The ribbon code just looked for atoms CA or C5' or P and did not consider whether the residue polymer type was amino acid or nucleic acid. I made it only use CA if the polymer type is amino acid and only use C5' or P if the polymer type is nucleic acid.
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Confirming the obvious: changing the name of the CA to something else ("CA99") and redrawing the cartoon leads to a correct ribbon path.