id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4424 Missing bonds hello@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19041 ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC) Description The display of a molecule is missing links between c-c and c-o randomly. With thanks Vishal K Sahu 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 D:/MDD/MDA5-SAB-2x23-w5/out.pdbqt Summary of feedback from opening D:/MDD/MDA5-SAB-2x23-w5/out.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -9.1 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 4 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 157 messages similar to the above omitted Opened out.pdbqt containing 9 structures (270 atoms, 279 bonds) > open D:/MDD/MDA5-SAB-2x23-w5/protein.pdbqt Chain information for protein.pdbqt #2 --- Chain | Description A B E G | No description available Opened protein.pdbqt containing 1 structures (10016 atoms, 10187 bonds) > hide #1.2 models > hide #1.3 models > hide #1.4 models > hide #1.5 models > hide #1.6 models > hide #1.7 models > hide #1.8 models > hide #1.9 models > close #1.2-9 > select #1.1 30 atoms, 31 bonds, 1 residue, 1 model selected No model chosen to save relative to No model chosen to save relative to > save D:/Desktop/lig.pdb models #1 relModel #1.1 > open D:/Desktop/lig.pdb Summary of feedback from opening D:/Desktop/lig.pdb --- warning | Ignored bad PDB record found on line 31 END > hide #1.1 models > show #1.1 models > hide #1.1 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hbonds #2-3 987 hydrogen bonds found > close #1 > select #3 30 atoms, 31 bonds, 1 residue, 1 model selected > select #2 10016 atoms, 10187 bonds, 987 pseudobonds, 1081 residues, 2 models selected > select #3 30 atoms, 31 bonds, 1 residue, 1 model selected > select #4 987 pseudobonds, 1 model selected > select #3 30 atoms, 31 bonds, 1 residue, 1 model selected > select #2 10016 atoms, 10187 bonds, 987 pseudobonds, 1081 residues, 2 models selected > ~select #4 10016 atoms, 10187 bonds, 1081 residues, 1 model selected > select #3 30 atoms, 31 bonds, 1 residue, 1 model selected > hbonds sel 0 hydrogen bonds found > select #2 10016 atoms, 10187 bonds, 1081 residues, 1 model selected > ~select #2 Nothing selected > ~select #4 Nothing selected > close #4 > select #3 30 atoms, 31 bonds, 1 residue, 1 model selected > select #2 10016 atoms, 10187 bonds, 1081 residues, 1 model selected > select #3 30 atoms, 31 bonds, 1 residue, 1 model selected > select #2 10016 atoms, 10187 bonds, 1081 residues, 1 model selected > select #3 30 atoms, 31 bonds, 1 residue, 1 model selected > select #2 10016 atoms, 10187 bonds, 1081 residues, 1 model selected > select #3 #2 10046 atoms, 10218 bonds, 1082 residues, 2 models selected > hbonds sel 987 hydrogen bonds found > hide #3 models > hide #2 models > hide #1 models > show #3 models > show #2 models > show #1 models > ~select #2 30 atoms, 31 bonds, 1 residue, 1 model selected > close > open D:/MDD/MDA5-SAB-2x23-w5/ligand.pdbqt Summary of feedback from opening D:/MDD/MDA5-SAB-2x23-w5/ligand.pdbqt --- warnings | Ignored bad PDB record found on line 1 REMARK 4 active torsions: Ignored bad PDB record found on line 2 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 3 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 4 REMARK 2 A between atoms: C_10 and O_17 Ignored bad PDB record found on line 5 REMARK 3 A between atoms: C_13 and C_19 12 messages similar to the above omitted Opened ligand.pdbqt containing 1 structures (30 atoms, 31 bonds) > close > open D:/MDD/MDA5-SAB-2x23-w5/out.pdbqt Summary of feedback from opening D:/MDD/MDA5-SAB-2x23-w5/out.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -9.1 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 4 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 157 messages similar to the above omitted Opened out.pdbqt containing 9 structures (270 atoms, 279 bonds) > close #1.2-9 > hbonds 0 hydrogen bonds found > interfaces ~solvent 0 buried areas: > style sphere Changed 30 atom styles No Surface models open > show surfaces > style stick Changed 30 atom styles > style sphere Changed 30 atom styles > style sphere Changed 30 atom styles > style ball Changed 30 atom styles > style ball Changed 30 atom styles > nucleotides atoms > style nucleic stick Changed 0 atom styles > style stick Changed 30 atom styles > transparency 50 > select :0@C 25 atoms, 24 bonds, 1 residue, 1 model selected > select :0@C 25 atoms, 24 bonds, 1 residue, 1 model selected > select none Expected an objects specifier or a keyword > select 0 Expected an objects specifier or a keyword > select all 30 atoms, 31 bonds, 1 residue, 2 models selected > select invert Expected an objects specifier or a keyword > select off Expected an objects specifier or a keyword > ~select #1 1 model selected > ~select Nothing selected > select 30 atoms, 31 bonds, 1 residue, 2 models selected > ~select Nothing selected > select 30 atoms, 31 bonds, 1 residue, 2 models selected > addh Summary of feedback from adding hydrogens to out.pdbqt #1.1 --- warning | Unknown hybridization for atom (C) of residue type UNK; not adding hydrogens to it notes | Chain-initial residues that are actual N termini: 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: 0 hydrogen bonds 17 hydrogens added > close > open D:/MDD/MDA5-SAB-2x23-w5/out.pdbqt Summary of feedback from opening D:/MDD/MDA5-SAB-2x23-w5/out.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -9.1 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 4 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 157 messages similar to the above omitted Opened out.pdbqt containing 9 structures (270 atoms, 279 bonds) > hide #1.1-9 target m > show #1.2 models > show #1.1 models > hide #1.2 models > hide #1.1 models > show #1.2 models > hide #1.2 models > show #1.3 models > show #1.4 models > hide #1.3 models > addh Summary of feedback from adding hydrogens to multiple structures --- warnings | Unknown hybridization for atom (C) of residue type UNK; not adding hydrogens to it Unknown hybridization for atom (C) of residue type UNK; not adding hydrogens to it Unknown hybridization for atom (C) of residue type UNK; not adding hydrogens to it Unknown hybridization for atom (C) of residue type UNK; not adding hydrogens to it Unknown hybridization for atom (C) of residue type UNK; not adding hydrogens to it 4 messages similar to the above omitted notes | Chain-initial residues that are actual N termini: 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: 0 hydrogen bonds Chain-initial residues that are actual N termini: 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: 0 hydrogen bonds Chain-initial residues that are actual N termini: 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: 0 hydrogen bonds Chain-initial residues that are actual N termini: 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: 0 hydrogen bonds Chain-initial residues that are actual N termini: 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: 0 hydrogen bonds Chain-initial residues that are actual N termini: 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: 0 hydrogen bonds Chain-initial residues that are actual N termini: 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: 0 hydrogen bonds Chain-initial residues that are actual N termini: 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: 0 hydrogen bonds Chain-initial residues that are actual N termini: 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: 0 hydrogen bonds 153 hydrogens added OpenGL version: 3.3.0 - Build 27.20.100.8681 OpenGL renderer: Intel(R) UHD Graphics 630 OpenGL vendor: Intel Manufacturer: HP Model: HP Desktop Pro G1 MT OS: Microsoft Windows 10 Pro (Build 19042) Memory: 4,147,757,056 MaxProcessMemory: 137,438,953,344 CPU: 6 Intel(R) Core(TM) i5-8500 CPU @ 3.00GHz"" 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: 2.1.3 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-Cytoscape: 0.1 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-Label: 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-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-RMF: 0.9 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: 1.2.1 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 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 gdcm: 2.8.8 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 MolecularDynamicsViewer: 1.1 msgpack: 1.0.0 netifaces: 0.10.9 networkx: 2.4 numexpr: 2.7.1 numpy: 1.18.5+mkl numpydoc: 1.0.0 openvr: 1.12.501 packaging: 20.4 parso: 0.7.1 pickleshare: 0.7.5 Pillow: 7.1.2 pip: 20.2.2 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.7 psutil: 5.7.0 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 pywin32: 228 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 WMI: 1.5.1 File attachment: chimera-bug.pdf }}} [attachment:""chimera-bug.pdf""] " defect feedback normal Input/Output all ChimeraX