id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
14498	ISOLDE: possible error in MD template	ray@…	Tristan Croll	"{{{
The following bug report has been submitted:
Platform:        Linux-6.2.0-39-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
ChimeraX (1.6, 1.6.1, 1.7.1). Load map and PDB structure. Start ISOLDE. Open Unparameterised Residues tool. Select a SER residue. Attempt to parameterise with default (SER). Error thrown:

""Failed to add atoms ['HB2', 'HB3'] to atom C because this will lead to having 5 atoms attached, which is more than its assigned geometry can support. This is probably due to an error in the MD template (SER). If this template is built into ISOLDE, please report this using Help/Report a bug""

This only started happening recently. Occurs on multiple systems, at different sites (work/home).

OpenGL version: 3.3.0 NVIDIA 535.154.05
OpenGL renderer: NVIDIA RTX A4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=cinnamon
XDG_SESSION_DESKTOP=cinnamon
XDG_CURRENT_DESKTOP=X-Cinnamon
DISPLAY=:0
Manufacturer: Gigabyte Technology Co., Ltd.
Model: B550M AORUS PRO-P
OS: Linux Mint 21.2 Victoria
Architecture: 64bit ELF
Virtual Machine: none
CPU: 16 AMD Ryzen 7 5700G with Radeon Graphics
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            62Gi       9.7Gi        41Gi       151Mi        10Gi        51Gi
	Swap:          2.0Gi          0B       2.0Gi

Graphics:
	01:00.0 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: 2.14.0
   backcall: 0.2.0
   beautifulsoup4: 4.11.2
   blockdiag: 3.0.0
   blosc2: 2.0.0
   build: 0.10.0
   certifi: 2023.11.17
   cftime: 1.6.3
   charset-normalizer: 3.3.2
   ChimeraX-AddCharge: 1.5.13
   ChimeraX-AddH: 2.2.5
   ChimeraX-AlignmentAlgorithms: 2.0.1
   ChimeraX-AlignmentHdrs: 3.4.1
   ChimeraX-AlignmentMatrices: 2.1
   ChimeraX-Alignments: 2.12.2
   ChimeraX-AlphaFold: 1.0
   ChimeraX-AltlocExplorer: 1.1.1
   ChimeraX-AmberInfo: 1.0
   ChimeraX-Arrays: 1.1
   ChimeraX-Atomic: 1.49.1
   ChimeraX-AtomicLibrary: 12.1.5
   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: 1.3.2
   ChimeraX-ChemGroup: 2.0.1
   ChimeraX-Clashes: 2.2.4
   ChimeraX-Clipper: 0.22.4
   ChimeraX-ColorActions: 1.0.3
   ChimeraX-ColorGlobe: 1.0
   ChimeraX-ColorKey: 1.5.5
   ChimeraX-CommandLine: 1.2.5
   ChimeraX-ConnectStructure: 2.0.1
   ChimeraX-Contacts: 1.0.1
   ChimeraX-Core: 1.7.1
   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: 1.1.3
   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-ISOLDE: 1.7.1
   ChimeraX-ItemsInspection: 1.0.1
   ChimeraX-IUPAC: 1.0
   ChimeraX-Label: 1.1.8
   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: 1.1.4
   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: 2.6.1
   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: 1.5.14
   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: 1.13.1
   ChimeraX-PDB: 2.7.3
   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
   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: 1.12.4
   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: 1.33.3
   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-vrml: 1.0
   ChimeraX-VTK: 1.0
   ChimeraX-WavefrontOBJ: 1.0
   ChimeraX-WebCam: 1.0.2
   ChimeraX-WebServices: 1.1.3
   ChimeraX-Zone: 1.0.1
   colorama: 0.4.6
   comm: 0.2.1
   contourpy: 1.2.0
   cxservices: 1.2.2
   cycler: 0.12.1
   Cython: 0.29.33
   debugpy: 1.8.0
   decorator: 5.1.1
   distro: 1.7.0
   docutils: 0.19
   executing: 2.0.1
   filelock: 3.9.0
   fonttools: 4.47.2
   funcparserlib: 2.0.0a0
   glfw: 2.6.4
   grako: 3.16.5
   h5py: 3.10.0
   html2text: 2020.1.16
   idna: 3.6
   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: 5.7.1
   jupyterlab-widgets: 3.0.9
   kiwisolver: 1.4.5
   line-profiler: 4.0.2
   lxml: 4.9.2
   lz4: 4.3.2
   MarkupSafe: 2.1.4
   matplotlib: 3.7.2
   matplotlib-inline: 0.1.6
   msgpack: 1.0.4
   nest-asyncio: 1.6.0
   netCDF4: 1.6.2
   networkx: 3.1
   nibabel: 5.0.1
   nptyping: 2.5.0
   numexpr: 2.8.8
   numpy: 1.25.1
   openvr: 1.23.701
   packaging: 23.2
   ParmEd: 3.4.3
   parso: 0.8.3
   pep517: 0.13.0
   pexpect: 4.9.0
   pickleshare: 0.7.5
   pillow: 10.2.0
   pip: 23.0
   pkginfo: 1.9.6
   platformdirs: 4.1.0
   prompt-toolkit: 3.0.43
   psutil: 5.9.5
   ptyprocess: 0.7.0
   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
   pyzmq: 25.1.2
   qtconsole: 5.4.3
   QtPy: 2.4.1
   RandomWords: 0.4.0
   requests: 2.31.0
   scipy: 1.11.1
   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: 1.0.8
   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: 0.5.0
   tables: 3.8.0
   tcia-utils: 1.5.1
   tifffile: 2023.7.18
   tinyarray: 1.2.4
   tomli: 2.0.1
   tornado: 6.4
   traitlets: 5.9.0
   typing-extensions: 4.9.0
   tzdata: 2023.4
   urllib3: 2.1.0
   wcwidth: 0.2.13
   webcolors: 1.12
   wheel: 0.38.4
   wheel-filename: 1.4.1
   widgetsnbextension: 4.0.9


}}}
"	defect	assigned	normal		Third Party				Eric Pettersen Greg Couch				all	ChimeraX