Opened 12 months ago
Closed 12 months ago
#16147 closed defect (not a bug)
AddCharge: Hydrogen not bonded to exactly one other atom
Reported by: | Owned by: | Eric Pettersen | |
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Priority: | normal | Milestone: | |
Component: | Structure Editing | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Linux-6.8.0-45-generic-x86_64-with-glibc2.39 ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description (Describe the actions that caused this problem to occur here) Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /media/alrsong/x/workspace/BaiduSyncdisk/ZJU/MHC-I/UHRF1_dock.pdb Chain information for UHRF1_dock.pdb #1 --- Chain | Description A | No description available > ui tool show "Add Hydrogens" > addh #!1 Summary of feedback from adding hydrogens to UHRF1_dock.pdb #1 --- warnings | Not adding hydrogens to /A LYS 500 CD because it is missing heavy-atom bond partners Not adding hydrogens to /A LYS 568 CG because it is missing heavy-atom bond partners Not adding hydrogens to /A LYS 570 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A PHE 573 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A LYS 595 CD because it is missing heavy-atom bond partners 2 messages similar to the above omitted Skipped 10 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for UHRF1_dock.pdb (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A PRO 414 Chain-initial residues that are not actual N termini: /A CYS 497 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A HIS 619, /A GLY 483 Skipping possible acceptor with bad geometry: /A GLU 613 OE2 Wrong number of grandchild atoms for phi/psi acceptor /A GLU 613 OE2 Skipping possible acceptor with bad geometry: /A GLU 613 O Wrong number of grandchild atoms for phi/psi acceptor /A GLU 613 O Skipping possible acceptor with bad geometry: /A GLU 613 O Wrong number of grandchild atoms for phi/psi acceptor /A GLU 613 O Skipping possible acceptor with bad geometry: /A GLU 613 O Wrong number of grandchild atoms for phi/psi acceptor /A GLU 613 O Skipping possible acceptor with bad geometry: /A GLU 613 O Wrong number of grandchild atoms for phi/psi acceptor /A GLU 613 O 5 messages similar to the above omitted 162 hydrogen bonds Adding 'H' to /A CYS 497 /A HIS 619 is not terminus, removing H atom from 'C' 1082 hydrogens added > ui tool show ViewDockX No suitable models found for ViewDockX > toolshed show > ui tool show "Dock Prep" Starting dock prep Deleting solvent Deleting non-metal-complex ions Deleting non-current alt locs Filling out missing side chains /A LYS 500: phi -122.1, psi 155.2 trans /A LYS 568: phi -81.1, psi 123.3 trans /A LYS 570: phi -70.5, psi -30.8 trans /A PHE 573: phi -85.6, psi -167.4 trans /A LYS 595: phi -64.6, psi -40.5 trans /A LYS 599: phi -61.0, psi -44.5 trans /A LYS 600: phi -72.2, psi -35.3 trans /A GLU 613: phi -66.0, psi -32.7 trans /A HIS 619: phi -153.5, psi none trans Skipping possible acceptor with bad geometry: /A GLU 613 O Wrong number of grandchild atoms for phi/psi acceptor /A GLU 613 O [Repeated 33 time(s)] Skipped 34 atom(s) with bad connectivities; see log for details Applying LYS rotamer (chi angles: -58.7 -67.4 -174.2 -67.0) to /A LYS 500 Applying LYS rotamer (chi angles: -173.7 178.4 -68.9 -68.5) to /A LYS 568 Applying LYS rotamer (chi angles: -69.7 -179.1 -177.9 -64.9) to /A LYS 570 Applying PHE rotamer (chi angles: -66.8 118.2) to /A PHE 573 Applying LYS rotamer (chi angles: -68.3 -171.6 -72.2 -66.9) to /A LYS 595 Applying LYS rotamer (chi angles: -68.3 -171.6 -72.2 -66.9) to /A LYS 599 Applying LYS rotamer (chi angles: -177.4 77.6 -89.8 -82.1) to /A LYS 600 Applying GLU rotamer (chi angles: -65.3 82.2 1.8) to /A GLU 613 Applying HIS rotamer (chi angles: 65.4 -79.5) to /A HIS 619 Summary of feedback from adding hydrogens to UHRF1_dock.pdb #1 --- warnings | Not adding hydrogens to /A GLU 613 CA because it is missing heavy-atom bond partners Skipped 7 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for UHRF1_dock.pdb (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A PRO 414 Chain-initial residues that are not actual N termini: /A CYS 497 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A HIS 619, /A GLY 483 Skipping possible acceptor with bad geometry: /A GLU 613 O Wrong number of grandchild atoms for phi/psi acceptor /A GLU 613 O Skipping possible acceptor with bad geometry: /A GLU 613 O Wrong number of grandchild atoms for phi/psi acceptor /A GLU 613 O Skipping possible acceptor with bad geometry: /A GLU 613 O Wrong number of grandchild atoms for phi/psi acceptor /A GLU 613 O Skipping possible acceptor with bad geometry: /A GLU 613 O Wrong number of grandchild atoms for phi/psi acceptor /A GLU 613 O Skipping possible acceptor with bad geometry: /A GLU 613 O Wrong number of grandchild atoms for phi/psi acceptor /A GLU 613 O 2 messages similar to the above omitted 170 hydrogen bonds /A HIS 619 is not terminus, removing H atom from 'C' 82 hydrogens added Closest equivalent command: addcharge standardizeResidues none Using Amber 20 recommended default charges and atom types for standard residues Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/add_charge/tool.py", line 120, in add_charges self._finish_add_charge(residues) File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/add_charge/tool.py", line 146, in _finish_add_charge non_std = add_standard_charges(self.session, residues=residues, **params) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/add_charge/charge.py", line 107, in add_standard_charges raise ChargeError("Hydrogen %s not bonded to exactly one other atom" % a) chimerax.add_charge.charge.ChargeError: Hydrogen /A GLU 613 H not bonded to exactly one other atom chimerax.add_charge.charge.ChargeError: Hydrogen /A GLU 613 H not bonded to exactly one other atom File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/add_charge/charge.py", line 107, in add_standard_charges raise ChargeError("Hydrogen %s not bonded to exactly one other atom" % a) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 535.183.01 OpenGL renderer: NVIDIA GeForce RTX 4090/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: xcb XDG_SESSION_TYPE=x11 DESKTOP_SESSION=ubuntu XDG_SESSION_DESKTOP=ubuntu XDG_CURRENT_DESKTOP=ubuntu:GNOME DISPLAY=:0 Manufacturer: ASUS Model: System Product Name OS: Ubuntu 24.04 Noble Numbat Architecture: 64bit ELF Virtual Machine: none CPU: 32 13th Gen Intel(R) Core(TM) i9-13900K Cache Size: 36864 KB Memory: total used free shared buff/cache available Mem: 125Gi 10Gi 3.7Gi 458Mi 113Gi 115Gi Swap: 186Gi 1.5Mi 186Gi Graphics: 01:00.0 VGA compatible controller [0300]: NVIDIA Corporation AD102 [GeForce RTX 4090] [10de:2684] (rev a1) Subsystem: ASUSTeK Computer Inc. AD102 [GeForce RTX 4090] [1043:889c] Kernel driver in use: nvidia 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: 2024.6.2 cftime: 1.6.4 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: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 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: 1.2.7 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: 1.0.5 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: 1.8 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: 1.2.4 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-LinuxSupport: 1.0.1 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: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 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: 1.13.5 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: 3.0.15 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: 1.16.5 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: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 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 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 distro: 1.9.0 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 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: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 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: 24.1 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 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 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: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 12 months ago
Component: | Unassigned → Structure Editing |
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Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Summary: | ChimeraX bug report submission → AddCharge: Hydrogen not bonded to exactly one other atom |
comment:2 by , 12 months ago
Resolution: | → not a bug |
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Status: | accepted → closed |
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Either mangled CONECT records or badly incomplete structure