id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6387 Found H-bonds differ Qchao.sun@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.4.dev202203160044 (2022-03-16 00:44:37 UTC) Description ""Tool-structure editing-Hbond"", could not return any H bonds. While the H-bonds in ""Molecule Display-H bonds"" could give the right H bonds. Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.4.dev202203160044 (2022-03-16) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/Qchao/Downloads/Bioluminescence/RLuc_CTZ.pdb RLuc_CTZ.pdb title: Crystal structures of the luciferase and green fluorescent protein from renilla reniformis [more info...] Chain information for RLuc_CTZ.pdb #1 --- Chain | Description | UniProt A B | renilla-TYPE luciferase | LUCI_RENRE Non-standard residues in RLuc_CTZ.pdb #1 --- CEI — N-[3-benzyl-5-(4-hydroxyphenyl)pyrazin-2-yl]-2-(4-hydroxyphenyl)acetamide (coelenteramide) > ui tool show H-Bonds > select /A:290 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 45 atoms, 45 bonds, 5 residues, 1 model selected > select up 1274 atoms, 1305 bonds, 156 residues, 1 model selected > select up 1326 atoms, 1356 bonds, 163 residues, 1 model selected > select up 2503 atoms, 2572 bonds, 306 residues, 1 model selected > select up 2762 atoms, 2606 bonds, 535 residues, 1 model selected > select up 5521 atoms, 5212 bonds, 1067 residues, 1 model selected > select down 2762 atoms, 2606 bonds, 535 residues, 1 model selected > delete atoms sel > delete bonds sel > select /B:502@C11 1 atom, 1 residue, 1 model selected > select up 31 atoms, 34 bonds, 1 residue, 1 model selected > ui tool show H-Bonds > hbonds sel dashes 6 showDist true interModel false intraModel false distSlop > 4.0 angleSlop 90.0 twoColors true intraMol false intraRes false select true > reveal true retainCurrent true 0 hydrogen bonds found 0 strict hydrogen bonds found > hbonds reveal true 897 hydrogen bonds found > select /B:502@C11 1 atom, 1 residue, 1 model selected > select up 31 atoms, 34 bonds, 1 residue, 1 model selected > ui tool show H-Bonds > hbonds sel dashes 6 showDist true interModel false intraModel false distSlop > 4.0 angleSlop 90.0 twoColors true intraMol false intraRes false select true > reveal true retainCurrent true 0 hydrogen bonds found 0 strict hydrogen bonds found > toolshed show Downloading bundle ChimeraX_ISOLDE-1.3-cp39-cp39-macosx_10_13_x86_64.whl Downloading bundle /Users/Qchao/Downloads/ChimeraX_ISOLDE-1.3-cp39-cp39-macosx_10_13_x86_64.whl [Repeated 4 time(s)] > ~hbonds > addh Summary of feedback from adding hydrogens to RLuc_CTZ.pdb #1 --- notes | No usable SEQRES records for RLuc_CTZ.pdb (#1) chain B; guessing termini instead Chain-initial residues that are actual N termini: /B SER 3 Chain-initial residues that are not actual N termini: /B GLU 155 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /B GLU 310, /B SER 152 898 hydrogen bonds Adding 'H' to /B GLU 155 /B GLU 310 is not terminus, removing H atom from 'C' 2950 hydrogens added > select /B:502@C11 1 atom, 1 residue, 1 model selected > select up 52 atoms, 55 bonds, 1 residue, 1 model selected > ui tool show H-Bonds > hbonds sel dashes 6 showDist true interModel false intraModel false distSlop > 4.0 angleSlop 90.0 twoColors true intraMol false intraRes false select true > reveal true retainCurrent true 0 hydrogen bonds found 0 strict hydrogen bonds found > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 52 atoms, 55 bonds, 1 residue, 1 model selected > hbonds sel reveal true 2 hydrogen bonds found > hbonds sel dashes 6 showDist true interModel false intraModel false distSlop > 4.0 angleSlop 90.0 twoColors true intraMol false intraRes false select true > reveal true retainCurrent true 0 hydrogen bonds found 0 strict hydrogen bonds found Downloading bundle ChimeraX_ISOLDE-1.3-cp39-cp39-macosx_10_13_x86_64.whl [Repeated 1 time(s)]Downloading bundle /Users/Qchao/Downloads/ChimeraX_ISOLDE-1.3-cp39-cp39-macosx_10_13_x86_64.whl OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Locale: UTF-8 Qt version: PyQt6 6.2.3, Qt 6.2.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Processor Name: Unknown Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 10 L2 Cache: 20 MB Memory: 32 GB Software: System Software Overview: System Version: macOS 12.2.1 (21D62) Kernel Version: Darwin 21.3.0 Time since boot: 1 day 8:38 Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal DELL SE2419H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.5.30 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.36.2 ChimeraX-AtomicLibrary: 6.1.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.1 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4.dev202203160044 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 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: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 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 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.5 ChimeraX-ModelPanel: 1.3.2 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.8 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.9 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.16.3 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 ChimeraX-VIPERdb: 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: 0.4.4 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.5.1 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.30.0 funcparserlib: 1.0.0a0 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.26 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.9.2 kiwisolver: 1.4.0 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.4 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.0 ParmEd: 3.4.3 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.28 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.7 PyQt6-commercial: 6.2.3 PyQt6-sip: 13.2.0 PyQt6-WebEngine-commercial: 6.2.1 python-dateutil: 2.8.2 pytz: 2021.3 pyzmq: 22.3.0 qtconsole: 5.2.2 QtPy: 2.0.1 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.8 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 }}} " defect closed normal Structure Analysis not a bug all ChimeraX