id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4018 ISOLDE: OpenMM: find_glycan_template_name_and_link: multiple bonds between residues kartik.manne@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.1 (2020-09-09) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /home/kartikmanne/Documents/DH898.1/DH898.1_apotrimer/DH898p1_fitModel_P67_J2290_apoTrimer-1_real_space_refined_RR11.pdb Chain information for DH898p1_fitModel_P67_J2290_apoTrimer-1_real_space_refined_RR11.pdb #1 --- Chain | Description a c e | No description available b d f | No description available > set bgColor white > open > /home/kartikmanne/Documents/DH898.1/DH898.1_apotrimer/cryosparc_P67_J229__localfilter.mrc Opened cryosparc_P67_J229__localfilter.mrc, grid size 256,256,256, pixel 1.07, shown at level 0.313, step 1, values float32 > clipper associate #2 toModel #1 Chain information for DH898p1_fitModel_P67_J2290_apoTrimer-1_real_space_refined_RR11.pdb --- Chain | Description 1.2/a 1.2/c 1.2/e | No description available 1.2/b 1.2/d 1.2/f | No description available > isolde start > set selectionWidth 4 Done loading forcefield > clipper spotlight radius 32.00 > clipper spotlight radius 32.00 > select #1 29361 atoms, 29835 bonds, 6 pseudobonds, 1929 residues, 13 models selected Traceback (most recent call last): File ""/home/kartikmanne/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/isolde.py"", line 2707, in _start_sim_or_toggle_pause self.start_sim() File ""/home/kartikmanne/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/isolde.py"", line 2727, in start_sim self.params, self.sim_params, excluded_residues = self.ignored_residues) File ""/home/kartikmanne/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 616, in __init__ raise e File ""/home/kartikmanne/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 595, in __init__ isolde.forcefield_mgr) File ""/home/kartikmanne/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1327, in __init__ template_dict = find_residue_templates(sim_construct.all_residues, ff, ligand_db=ligand_db, logger=session.logger) File ""/home/kartikmanne/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 3105, in find_residue_templates tname, prot_res = find_glycan_template_name_and_link(sugar) File ""/home/kartikmanne/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/openmm/amberff/glycam.py"", line 250, in find_glycan_template_name_and_link r.chain_id, r.number, n.chain_id, n.number RuntimeError: Residue a515 has multiple bonds to neighbor a516 RuntimeError: Residue a515 has multiple bonds to neighbor a516 File ""/home/kartikmanne/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/openmm/amberff/glycam.py"", line 250, in find_glycan_template_name_and_link r.chain_id, r.number, n.chain_id, n.number See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 430.40 OpenGL renderer: GeForce RTX 2080 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: TYAN Model: B7105F48TV8HR-2T-G OS: CentOS Linux 7 Core Architecture: 64bit ELF CPU: 64 Intel(R) Xeon(R) Silver 4216 CPU @ 2.10GHz Cache Size: 22528 KB Memory: total used free shared buff/cache available Mem: 187G 6.6G 175G 170M 5.5G 179G Swap: 9G 0B 9G Graphics: 04:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41) Subsystem: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] Kernel driver in use: ast PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.9 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.8.0 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.6.20 chardet: 3.0.4 ChimeraX-AddH: 2.1.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.6.1 ChimeraX-AtomSearch: 2.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.0.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.0 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.0 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.0 ChimeraX-Clipper: 0.15.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-CommandLine: 1.1.3 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.1 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.0.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-DataFormats: 1.0 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.0 ChimeraX-Hbonds: 2.0 ChimeraX-Help: 1.0 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.0 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0 ChimeraX-ISOLDE: 1.1.0 ChimeraX-Label: 1.0 ChimeraX-LinuxSupport: 1.0 ChimeraX-ListInfo: 1.0 ChimeraX-Log: 1.1.1 ChimeraX-LookingGlass: 1.1 ChimeraX-Map: 1.0.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.1 ChimeraX-MDcrds: 2.0 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.0 ChimeraX-mmCIF: 2.2 ChimeraX-MMTF: 2.0 ChimeraX-Modeller: 1.0 ChimeraX-ModelPanel: 1.0 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.0 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0 ChimeraX-OpenCommand: 1.2.1 ChimeraX-PDB: 2.1 ChimeraX-PDBBio: 1.0 ChimeraX-Phenix: 0.1 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0 ChimeraX-PubChem: 2.0 ChimeraX-Read-Pbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.0 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.2 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.0.4 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.0 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.0 ChimeraX-ToolshedUtils: 1.0 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.2.3 ChimeraX-uniprot: 2.0 ChimeraX-ViewDockX: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.20 decorator: 4.4.2 distlib: 0.3.1 distro: 1.5.0 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.16 imagecodecs: 2020.5.30 imagecodecs-lite: 2020.1.31 imagesize: 1.2.0 ipykernel: 5.3.0 ipython: 7.15.0 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.3 jupyter-core: 4.6.3 kiwisolver: 1.2.0 line-profiler: 2.1.2 lxml: 4.5.1 MarkupSafe: 1.1.1 matplotlib: 3.2.1 msgpack: 1.0.0 netifaces: 0.10.9 networkx: 2.4 numexpr: 2.7.1 numpy: 1.18.5 numpydoc: 1.0.0 openvr: 1.12.501 packaging: 20.4 parso: 0.7.1 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 7.1.2 pip: 20.2.3 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.7 psutil: 5.7.0 ptyprocess: 0.6.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.6.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.12.3 PyQt5-sip: 4.19.19 PyQtWebEngine-commercial: 5.12.1 python-dateutil: 2.8.1 pytz: 2020.1 pyzmq: 19.0.2 qtconsole: 4.7.4 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.4.1 setuptools: 49.4.0 sfftk-rw: 0.6.6.dev0 six: 1.15.0 snowballstemmer: 2.0.0 sortedcontainers: 2.2.2 Sphinx: 3.1.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 1.0.3 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.4 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.6.3 tinyarray: 1.2.2 tornado: 6.0.4 traitlets: 5.0.4 urllib3: 1.25.10 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.34.2 }}} " defect closed normal Third Party fixed Eric Pettersen all ChimeraX