Opened 2 months ago
Closed 2 months ago
#18417 closed defect (duplicate)
ChargeError not caught
Reported by: | Owned by: | Eric Pettersen | |
---|---|---|---|
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-6.8.0-65-generic-x86_64-with-glibc2.35 ChimeraX Version: 1.8rc202405160048 (2024-05-16 00:48:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x00007e291ffe7640 (most recent call first): File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 324 in wait File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 622 in wait File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1392 in run File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap Current thread 0x00007e2a1f41fb80 (most recent call first): File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 460 in File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 460 in _prep_add File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 182 in hbond_add_hydrogens File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 176 in hbond_add_hydrogens File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 77 in cmd_addh File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/addh/dock_prep.py", line 55 in run_for_dock_prep File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/addh/dock_prep.py", line 48 in File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/addh/tool.py", line 206 in add_h File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 285 in event_loop File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1006 in init File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1169 in File "", line 88 in _run_code File "", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, chimerax.pdb_lib._load_libs, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 52) ===== Log before crash start ===== Startup Messages --- notes | available bundle cache has not been initialized yet Database-fetch provider 'redo' in bundle Map specified unknown data format 'MTZ' UCSF ChimeraX version: 1.8rc202405160048 (2024-05-16) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /home/mobd-s/Documents/projects/Protup/receptor.pdb Chain information for receptor.pdb #1 --- Chain | Description A | No description available > select /A 2084 atoms, 2008 bonds, 219 residues, 1 model selected > ui tool show "Dock Prep" Starting dock prep Deleting solvent Deleting non-metal-complex ions Deleting non-current alt locs Summary of feedback from adding hydrogens to receptor.pdb #1 --- warnings | Not adding hydrogens to /A TRP 42 CA because it is missing heavy-atom bond partners Not adding hydrogens to /A TRP 42 C because it is missing heavy-atom bond partners Not adding hydrogens to /A HIS 76 CA because it is missing heavy-atom bond partners Not adding hydrogens to /A HIS 76 C because it is missing heavy-atom bond partners Not adding hydrogens to /A HIS 76 CB because it is missing heavy-atom bond partners 48 messages similar to the above omitted Skipped 14 atom(s) with bad connectivities; see log for details The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: /A GLU 176 N notes | No usable SEQRES records for receptor.pdb (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A GLN 38 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A LYS 256 Skipping possible acceptor with bad geometry: /A PHE 87 O Wrong number of grandchild atoms for phi/psi acceptor /A PHE 87 O Skipping possible acceptor with bad geometry: /A PHE 87 O Wrong number of grandchild atoms for phi/psi acceptor /A PHE 87 O Skipping possible acceptor with bad geometry: /A ALA 55 O Wrong number of grandchild atoms for phi/psi acceptor /A ALA 55 O Skipping possible acceptor with bad geometry: /A PHE 87 O Wrong number of grandchild atoms for phi/psi acceptor /A PHE 87 O Skipping possible acceptor with bad geometry: /A LEU 119 O Wrong number of grandchild atoms for phi/psi acceptor /A LEU 119 O 9 messages similar to the above omitted 119 hydrogen bonds /A LYS 256 is not terminus, removing H atom from 'C' 1529 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 127, in add_standard_charges raise ChargeError("Hydrogen %s bonded to non-heavy atom %s" % (h, heavy)) chimerax.add_charge.charge.ChargeError: Hydrogen /A GLU 39 HN bonded to non- heavy atom /A GLU 39 1HN chimerax.add_charge.charge.ChargeError: Hydrogen /A GLU 39 HN bonded to non- heavy atom /A GLU 39 1HN File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/add_charge/charge.py", line 127, in add_standard_charges raise ChargeError("Hydrogen %s bonded to non-heavy atom %s" % (h, heavy)) See log for complete Python traceback. > 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 256: phi -100.0, psi none trans The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: /A GLU 176 N Applying LYS rotamer (chi angles: -68.5 176.2 69.4 177.3) to /A LYS 256 Summary of feedback from adding hydrogens to receptor.pdb #1 --- warnings | Not adding hydrogens to /A TRP 42 CA because it is missing heavy-atom bond partners Not adding hydrogens to /A TRP 42 C because it is missing heavy-atom bond partners Not adding hydrogens to /A HIS 76 CA because it is missing heavy-atom bond partners Not adding hydrogens to /A HIS 76 C because it is missing heavy-atom bond partners Not adding hydrogens to /A HIS 76 CB because it is missing heavy-atom bond partners 49 messages similar to the above omitted Skipped 14 atom(s) with bad connectivities; see log for details The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: /A GLU 176 N notes | No usable SEQRES records for receptor.pdb (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A GLN 38 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A LYS 256 Skipping possible acceptor with bad geometry: /A PHE 87 O Wrong number of grandchild atoms for phi/psi acceptor /A PHE 87 O Skipping possible acceptor with bad geometry: /A PHE 87 O Wrong number of grandchild atoms for phi/psi acceptor /A PHE 87 O Skipping possible acceptor with bad geometry: /A ALA 55 O Wrong number of grandchild atoms for phi/psi acceptor /A ALA 55 O Skipping possible acceptor with bad geometry: /A PHE 87 O Wrong number of grandchild atoms for phi/psi acceptor /A PHE 87 O Skipping possible acceptor with bad geometry: /A LEU 119 O Wrong number of grandchild atoms for phi/psi acceptor /A LEU 119 O 9 messages similar to the above omitted 118 hydrogen bonds /A LYS 256 is not terminus, removing H atom from 'C' 11 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 127, in add_standard_charges raise ChargeError("Hydrogen %s bonded to non-heavy atom %s" % (h, heavy)) chimerax.add_charge.charge.ChargeError: Hydrogen /A GLU 39 HN bonded to non- heavy atom /A GLU 39 1HN chimerax.add_charge.charge.ChargeError: Hydrogen /A GLU 39 HN bonded to non- heavy atom /A GLU 39 1HN File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/add_charge/charge.py", line 127, in add_standard_charges raise ChargeError("Hydrogen %s bonded to non-heavy atom %s" % (h, heavy)) See log for complete Python traceback. > open /home/mobd-s/Documents/projects/Protup/temozolomide_docked.pdb Chain information for temozolomide_docked.pdb #2 --- Chain | Description A | No description available > delete atoms sel > delete bonds sel > select ::name="UNL" 16 atoms, 17 bonds, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > select > ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL" 2102 atoms, 2007 bonds, 220 residues, 2 models selected > ui tool show "Dock Prep" Starting dock prep Deleting solvent Deleting non-metal-complex ions Deleting non-current alt locs receptor.pdb #1/A LYS 256 is missing heavy backbone atoms Filling out missing side chains temozolomide_docked.pdb #2/A LYS 256: phi -100.0, psi none trans Applying LYS rotamer (chi angles: 66.8 82.3 -83.6 -67.0) to temozolomide_docked.pdb #2/A LYS 256 ===== Log before crash end ===== Log: Startup Messages --- notes | available bundle cache has not been initialized yet Database-fetch provider 'redo' in bundle Map specified unknown data format 'MTZ' UCSF ChimeraX version: 1.8rc202405160048 (2024-05-16) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 3.3.0 NVIDIA 570.158.01 OpenGL renderer: NVIDIA RTX A4000/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=:1 Manufacturer: Supermicro Model: AS -4023S-TRT OS: Ubuntu 22.04 Jammy Jellyfish Architecture: 64bit ELF Virtual Machine: none CPU: 32 AMD EPYC 7252 8-Core Processor Cache Size: 512 KB Memory: total used free shared buff/cache available Mem: 62Gi 7.4Gi 6.1Gi 411Mi 49Gi 54Gi Swap: 8.0Gi 11Mi 8.0Gi Graphics: 21:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA104GL [RTX A4000] [10de:24b0] (rev a1) Subsystem: NVIDIA Corporation GA104GL [RTX A4000] [10de:14ad] 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: 2024.2.2 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: 1.8rc202405160048 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-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 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 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: 4.51.0 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 MolecularDynamicsViewer: 1.6 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 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.43 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 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
Change History (2)
comment:1 by , 2 months ago
Component: | Unassigned → Structure Editing |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Summary: | ChimeraX bug report submission → ChargeError not caught |
comment:2 by , 2 months ago
Resolution: | → duplicate |
---|---|
Status: | accepted → closed |
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