Opened 16 months ago
Closed 16 months ago
#15546 closed defect (duplicate)
Color Actions: can only concatenate str (not "NoneType") to str
Reported by: | Owned by: | Eric Pettersen | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | General Controls | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Windows-10-10.0.22631 ChimeraX Version: 1.8rc202405150320 (2024-05-15 03:20:26 UTC) Description (Describe the actions that caused this problem to occur here) Log: Startup Messages --- notes | available bundle cache has not been initialized yet Database-fetch provider 'redo' in bundle Map specified unknown data format 'MTZ' You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.8rc202405150320 (2024-05-15) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open C:\\\Users\\\xrovur\\\Desktop\\\LRPPRC-SLIRP\\\Structures\\\8any.cif Summary of feedback from opening C:\\\Users\\\xrovur\\\Desktop\\\LRPPRC- SLIRP\\\Structures\\\8any.cif --- warnings | Atom HN10 is not in the residue template for SPM /AA:1702 Atom H103 is not in the residue template for SPD /AA:1703 Atom H103 is not in the residue template for SPD /A:3301 Atom H103 is not in the residue template for SPD /A:3302 Atom H103 is not in the residue template for SPD /A:3303 Atom HN13 is not in the residue template for PUT /A:3304 Atom H1 is not in the residue template for VAL /B:101 8any.cif title: Human mitochondrial ribosome in complex with LRPPRC, SLIRP, A-site, P-site, E-site tRNAs and mRNA [more info...] Chain information for 8any.cif #1 --- Chain | Description | UniProt 0 | 39S ribosomal protein L32, mitochondrial | RM32_HUMAN 1-188 1 | 39S ribosomal protein L33, mitochondrial | RM33_HUMAN 1-65 2 | 39S ribosomal protein L34, mitochondrial | RM34_HUMAN 1-92 3 | 39S ribosomal protein L35, mitochondrial | RM35_HUMAN 1-188 4 | 39S ribosomal protein L36, mitochondrial | RM36_HUMAN 1-103 5 | 39S ribosomal protein L37, mitochondrial | RM37_HUMAN 1-423 6 | 39S ribosomal protein L38, mitochondrial | RM38_HUMAN 1-380 7 | 39S ribosomal protein L39, mitochondrial | RM39_HUMAN 1-338 8 | 39S ribosomal protein L40, mitochondrial | RM40_HUMAN 1-206 9 | 39S ribosomal protein L41, mitochondrial | RM41_HUMAN 1-137 A | 16S mitochondrial rRNA | A0 | 28S ribosomal protein S34, mitochondrial | RT34_HUMAN 2-218 A1 | 28S ribosomal protein S35, mitochondrial | RT35_HUMAN 1-323 A2 | Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 | CHCH1_HUMAN 1-118 A3 | Aurora kinase A-interacting protein | AKIP_HUMAN 1-199 A4 | Pentatricopeptide repeat domain-containing protein 3, mitochondrial | PTCD3_HUMAN 1-689 A5 | Leucine-rich PPR motif-containing protein, mitochondrial | LPPRC_HUMAN 1-1394 A6 | SRA stem-loop-interacting RNA-binding protein, mitochondrial | SLIRP_HUMAN 1-109 AA | 12S mitochondrial rRNA | AB | 28S ribosomal protein S2, mitochondrial | RT02_HUMAN 1-296 AC | 28S ribosomal protein S24, mitochondrial | RT24_HUMAN 1-167 AD | 28S ribosomal protein S5, mitochondrial | RT05_HUMAN 1-430 AE | 28S ribosomal protein S6, mitochondrial | RT06_HUMAN 1-125 AF | 28S ribosomal protein S7, mitochondrial | RT07_HUMAN 1-242 AG | 28S ribosomal protein S9, mitochondrial | RT09_HUMAN 1-396 AH | 28S ribosomal protein S10, mitochondrial | RT10_HUMAN 1-201 AI | 28S ribosomal protein S11, mitochondrial | RT11_HUMAN 1-194 AJ | 28S ribosomal protein S12, mitochondrial | RT12_HUMAN 1-138 AK | 28S ribosomal protein S14, mitochondrial | RT14_HUMAN 1-128 AL | 28S ribosomal protein S15, mitochondrial | RT15_HUMAN 1-257 AM | 28S ribosomal protein S16, mitochondrial | RT16_HUMAN 1-137 AN | 28S ribosomal protein S17, mitochondrial | RT17_HUMAN 1-130 AO | 28S ribosomal protein S18b, mitochondrial | RT18B_HUMAN 1-258 AP | 28S ribosomal protein S18c, mitochondrial | RT18C_HUMAN 1-142 AQ | 28S ribosomal protein S21, mitochondrial | RT21_HUMAN 1-87 AR | 28S ribosomal protein S22, mitochondrial | RT22_HUMAN 1-360 AS | 28S ribosomal protein S23, mitochondrial | RT23_HUMAN 1-190 AT | 28S ribosomal protein S25, mitochondrial | RT25_HUMAN 1-173 AU | 28S ribosomal protein S26, mitochondrial | RT26_HUMAN 1-205 AV | 28S ribosomal protein S27, mitochondrial | RT27_HUMAN 1-414 AW | 28S ribosomal protein S28, mitochondrial | RT28_HUMAN 1-187 AX | 28S ribosomal protein S29, mitochondrial | RT29_HUMAN 1-398 AY | 28S ribosomal protein S31, mitochondrial | RT31_HUMAN 1-395 AZ | 28S ribosomal protein S33, mitochondrial | RT33_HUMAN 1-106 Aw | A/A-tRNA | Ax | P/P-tRNA | Ay | E/E-tRNA | Az | mRNA | B | mitochondrial tRNAVal | D | 39S ribosomal protein L2, mitochondrial | RM02_HUMAN 1-305 E | 39S ribosomal protein L3, mitochondrial | RM03_HUMAN 1-348 F | 39S ribosomal protein L4, mitochondrial | RM04_HUMAN 1-311 H | 39S ribosomal protein L9, mitochondrial | RM09_HUMAN 1-267 I | 39S ribosomal protein L10, mitochondrial | RM10_HUMAN 1-261 J | 39S ribosomal protein L11, mitochondrial | RM11_HUMAN 1-192 K | 39S ribosomal protein L13, mitochondrial | RM13_HUMAN 1-178 L | 39S ribosomal protein L14, mitochondrial | RM14_HUMAN 1-145 M | 39S ribosomal protein L15, mitochondrial | RM15_HUMAN 1-296 N | 39S ribosomal protein L16, mitochondrial | RM16_HUMAN 1-251 O | 39S ribosomal protein L17, mitochondrial | RM17_HUMAN 1-175 P | 39S ribosomal protein L18, mitochondrial | RM18_HUMAN 1-180 Q | 39S ribosomal protein L19, mitochondrial | RM19_HUMAN 1-292 R | 39S ribosomal protein L20, mitochondrial | RM20_HUMAN 1-149 S | 39S ribosomal protein L21, mitochondrial | RM21_HUMAN 1-205 T | 39S ribosomal protein L22, mitochondrial | RM22_HUMAN 1-206 U | 39S ribosomal protein L23, mitochondrial | RM23_HUMAN 1-153 V | 39S ribosomal protein L24, mitochondrial | RM24_HUMAN 1-216 W | 39S ribosomal protein L27, mitochondrial | RM27_HUMAN 1-148 X | 39S ribosomal protein L28, mitochondrial | RM28_HUMAN 1-256 Y | 39S ribosomal protein L47, mitochondrial | RM47_HUMAN 1-250 Z | 39S ribosomal protein L30, mitochondrial | RM30_HUMAN 1-161 a | 39S ribosomal protein L42, mitochondrial | RM42_HUMAN 1-142 b | 39S ribosomal protein L43, mitochondrial | RM43_HUMAN 1-215 c | 39S ribosomal protein L44, mitochondrial | RM44_HUMAN 1-332 d | 39S ribosomal protein L45, mitochondrial | RM45_HUMAN 1-306 e | 39S ribosomal protein L46, mitochondrial | RM46_HUMAN 1-279 f | 39S ribosomal protein L48, mitochondrial | RM48_HUMAN 1-212 g | 39S ribosomal protein L49, mitochondrial | RM49_HUMAN 1-166 h | 39S ribosomal protein L50, mitochondrial | RM50_HUMAN 1-158 i | 39S ribosomal protein L51, mitochondrial | RM51_HUMAN 1-128 j | 39S ribosomal protein L52, mitochondrial | RM52_HUMAN 1-123 k | 39S ribosomal protein L53, mitochondrial | RM53_HUMAN 1-112 l | 39S ribosomal protein L54, mitochondrial | RM54_HUMAN 1-138 m | 39S ribosomal protein L55, mitochondrial | RM55_HUMAN 1-128 o | Ribosomal protein 63, mitochondrial | RT63_HUMAN 1-102 p | Peptidyl-tRNA hydrolase ICT1, mitochondrial | ICT1_HUMAN 1-206 q | Growth arrest and DNA damage-inducible proteins-interacting protein 1 | G45IP_HUMAN 1-222 r | 39S ribosomal protein S18a, mitochondrial | RT18A_HUMAN 1-196 s | 39S ribosomal protein S30, mitochondrial | RT30_HUMAN 1-439 t u v w x y | 39S ribosomal protein L12, mitochondrial | RM12_HUMAN 1-198 z | 39S ribosomal protein L1, mitochondrial | RM01_HUMAN 1-325 Non-standard residues in 8any.cif #1 --- 1MA — 6-hydro-1-methyladenosine-5'-monophosphate 2MG — 2N-methylguanosine-5'-monophosphate 5F0 — (3~{S})-3-azanyl-4-methoxy-4-oxidanylidene-butanoic acid (1-methyl isoaspartic acid) 5MC — 5-methylcytidine-5'-monophosphate 5MU — 5-methyluridine 5'-monophosphate ATP — adenosine-5'-triphosphate AYA — N-acetylalanine B8T — 4-methyl, cytidine-5'-monophosphate FES — FE2/S2 (inorganic) cluster GDP — guanosine-5'-diphosphate K — potassium ion MA6 — 6N-dimethyladenosine-5'-monophoshate MG — magnesium ion NAD — nicotinamide-adenine-dinucleotide OMG — O2'-methylguanosine-5'-monophosphate OMU — O2'-methyluridine 5'-monophosphate PUT — 1,4-diaminobutane (putrescine) SAC — N-acetyl-serine SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34)) SPM — spermine THC — N-methylcarbonylthreonine VAL — valine ZN — zinc ion > hide atoms > show cartoons > set bgColor white > ui tool show "Color Actions" Traceback (most recent call last): File "C:\Users\xrovur\Downloads\Software\ChimeraX 1.8rc202405150320\bin\Lib\site-packages\chimerax\color_actions\tool.py", line 64, in <lambda> button.released.connect(lambda *, clr=spaced_name: self._color(clr)) ^^^^^^^^^^^^^^^^ File "C:\Users\xrovur\Downloads\Software\ChimeraX 1.8rc202405150320\bin\Lib\site-packages\chimerax\color_actions\tool.py", line 226, in _color commands.append("color " ^^^^^^^^ TypeError: can only concatenate str (not "NoneType") to str TypeError: can only concatenate str (not "NoneType") to str File "C:\Users\xrovur\Downloads\Software\ChimeraX 1.8rc202405150320\bin\Lib\site-packages\chimerax\color_actions\tool.py", line 226, in _color commands.append("color " ^^^^^^^^ See log for complete Python traceback. OpenGL version: 3.3.0 - Build 31.0.101.5186 OpenGL renderer: Intel(R) Iris(R) Xe Graphics OpenGL vendor: Intel Python: 3.11.4 Locale: en_US.cp1252 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: windows Manufacturer: HP Model: HP Elite x360 1040 14 inch G10 2-in-1 Notebook PC OS: Microsoft Windows 11 Enterprise (Build 22631) Memory: 33,974,132,736 MaxProcessMemory: 137,438,953,344 CPU: 12 13th Gen Intel(R) Core(TM) i7-1355U OSLanguage: en-US Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2024.2.2 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57 ChimeraX-AtomicLibrary: 14.0.4 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.4 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.4 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8rc202405150320 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.1 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 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: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.16 ChimeraX-ModelPanel: 1.5 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: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.4 ChimeraX-PDB: 2.7.5 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: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 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-Segmentations: 1.3.4 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.4 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 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: 1.39 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.1 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 comtypes: 1.4.1 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.51.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.2 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.10 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 24.0 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.43 psutil: 5.9.8 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pywin32: 306 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 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: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4 traitlets: 5.14.2 typing-extensions: 4.11.0 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.10 WMI: 1.5.1
Change History (2)
comment:1 by , 16 months ago
Component: | Unassigned → General Controls |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Summary: | ChimeraX bug report submission → Color Actions: can only concatenate str (not "NoneType") to str |
comment:2 by , 16 months ago
Resolution: | → duplicate |
---|---|
Status: | accepted → closed |
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