id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8001 H-bonds: More than 2 coplanar positions specified phil.cruz@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-12.6.1-arm64-arm-64bit ChimeraX Version: 1.5rc202210312311 (2022-10-31 23:11:39 UTC) Description Load the attached file into ChimeraX and then try to run either the Surface Coulombic or Surface Hydrophobicity presets for NIH 3D and you will get the error. I suspect it is related to colinear atoms or some other strangeness with the coordinates of one or more atoms. Found this from migration testing from 3DPX to NIH 3D. Log: UCSF ChimeraX version: 1.5rc202210312311 (2022-10-31) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/cruzp2/Downloads/out_15898.pdb Summary of feedback from opening /Users/cruzp2/Downloads/out_15898.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK --------------------PDB-to-VIPERdb MATRIX: ------------------------ Ignored bad PDB record found on line 2 REMARK -0.78508588 -0.5332578 0.3150814 Ignored bad PDB record found on line 3 REMARK 0.5156565 -0.28090696 0.80943786 Ignored bad PDB record found on line 4 REMARK -0.3431305 0.79795201 0.49551394 Ignored bad PDB record found on line 5 REMARK --------------------PDB-to-VIPERdb VECTOR: ------------------------ 10 messages similar to the above omitted Chain information for out_15898.pdb #1 --- Chain | Description A | No description available > preset nih3d ""surface hydrophobicity"" Using preset: NIH3D / Surface Hydrophobicity Changed 1662 atom radii, 1754 bond radii, 0 pseudobond radii Changed 0 pseudobond dashes Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff Color 'forest' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22 Color 'tangerine' is opaque: rgb(95.3%, 51.8%, 0%) hex: #f38400 Color 'grape' is opaque: rgb(64.3%, 0%, 86.7%) hex: #a400dd Color 'nih_blue' is opaque: rgb(12.5%, 33.3%, 54.1%) hex: #20558a Color 'jmol_carbon' is opaque: gray(56.5%) hex: #909090 Color 'bond_purple' is opaque: rgb(57.6%, 43.9%, 85.9%) hex: #9370db Color 'struts_grey' is opaque: gray(48%) hex: #7a7a7a Color 'carbon_grey' is opaque: gray(22.2%) hex: #393939 Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. Summary of feedback from adding hydrogens to out_15898.pdb #1 --- notes | No usable SEQRES records for out_15898.pdb (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A PHE 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A THR 196 Chain-final residues that are not actual C termini: Skipping possible acceptor with bad geometry: /A THR 23 O Wrong number of grandchild atoms for phi/psi acceptor /A THR 23 O Skipping possible acceptor with bad geometry: /A LYS 109 O Wrong number of grandchild atoms for phi/psi acceptor /A LYS 109 O Skipping possible acceptor with bad geometry: /A THR 94 O Wrong number of grandchild atoms for phi/psi acceptor /A THR 94 O Skipping possible acceptor with bad geometry: /A ASP 40 OD1 Wrong number of grandchild atoms for phi/psi acceptor /A ASP 40 OD1 Skipping possible acceptor with bad geometry: /A THR 131 O Wrong number of grandchild atoms for phi/psi acceptor /A THR 131 O 32 messages similar to the above omitted Traceback (most recent call last): File ""/Applications/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py"", line 1171, in run(ses, ""preset %s%s"" % (cat, StringArg.unparse(name.lower())))) File ""/Applications/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/preset_mgr/cmd.py"", line 50, in preset_cmd run_preset(session, cat, matches[0]) File ""/Applications/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/preset_mgr/cmd.py"", line 71, in run_preset session.presets.preset_function(category, preset)() File ""/Applications/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/preset_mgr/manager.py"", line 60, in cb bi.run_provider(self.session, name, self) File ""/Applications/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 386, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""/Applications/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/__init__.py"", line 1289, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""/Users/cruzp2/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/nih_presets/__init__.py"", line 22, in run_provider run_preset(session, name, mgr, **kw) File ""/Users/cruzp2/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/nih_presets/presets.py"", line 294, in run_preset mgr.execute(cmd) File ""/Applications/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/preset_mgr/manager.py"", line 88, in execute run(self.session, line, log=False) File ""/Applications/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/addh/cmd.py"", line 66, in cmd_addh add_h_func(session, structures, template=template, in_isolation=in_isolation, **prot_schemes) File ""/Applications/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/addh/cmd.py"", line 173, in hbond_add_hydrogens add_hydrogens(session, atoms, type_info_for_atom, naming_schemas, hydrogen_totals, File ""/Applications/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/addh/hbond.py"", line 248, in add_hydrogens hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop, angle_slop=rec_angle_slop) File ""/Applications/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/hbonds/hbond.py"", line 574, in find_hbonds donor_hyds = hyd_positions(donor_atom) File ""/Applications/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/hbonds/hydpos.py"", line 77, in hyd_positions bond_positions(heavy_loc, geom, bond_len, bonded_locs, coplanar=coplanar)) File ""/Applications/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/bond_geom.py"", line 73, in bond_positions return planar_pos(bondee, bonded, bond_len, coplanar, toward, away, toward2, away2) File ""/Applications/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/bond_geom.py"", line 129, in planar_pos pos = angle_pos(bondee, cur_bonded[0], bond_len, 120.0, coplanar) File ""/Applications/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/bond_geom.py"", line 231, in angle_pos raise ValueError(""More than 2 coplanar positions specified!"") ValueError: More than 2 coplanar positions specified! ValueError: More than 2 coplanar positions specified! File ""/Applications/ChimeraX-1.5-rc2022.10.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/bond_geom.py"", line 231, in angle_pos raise ValueError(""More than 2 coplanar positions specified!"") See log for complete Python traceback. OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M1 Max OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,2 Chip: Apple M1 Max Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 32 GB System Firmware Version: 8419.41.10 OS Loader Version: 7459.141.1 Software: System Software Overview: System Version: macOS 12.6.1 (21G217) Kernel Version: Darwin 21.6.0 Time since boot: 3 days 2:58 Graphics/Displays: Apple M1 Max: Chipset Model: Apple M1 Max Type: GPU Bus: Built-In Total Number of Cores: 24 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: Thunderbolt Display: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: Yes Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal BenQ GW2750H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.1.0 Babel: 2.10.3 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.4 ChimeraX-AddH: 2.2.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.6 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.41.5 ChimeraX-AtomicLibrary: 8.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.1 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.4 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.5rc202210312311 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3 ChimeraX-DockPrep: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 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-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.9 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.8 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.6 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.1 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-NIHPresets: 1.1.4 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.1 ChimeraX-PDB: 2.6.8 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 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: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 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: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.7.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.24.3 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.3 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 1.2.0 filelock: 3.7.1 fonttools: 4.38.0 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.33 imagecodecs: 2022.7.31 imagesize: 1.4.1 importlib-metadata: 5.0.0 ipykernel: 6.15.3 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 4.11.2 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.5.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.0 networkx: 2.8.5 numexpr: 2.8.4 numpy: 1.23.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.2.0 pip: 22.2.2 pkginfo: 1.8.3 prompt-toolkit: 3.0.31 psutil: 5.9.1 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.12.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 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: 2022.6 pyzmq: 24.0.1 qtconsole: 5.3.1 QtPy: 2.2.1 RandomWords: 0.4.0 requests: 2.28.1 scipy: 1.9.0 setuptools: 65.1.1 setuptools-scm: 7.0.5 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 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 stack-data: 0.6.0 tables: 3.7.0 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 typing-extensions: 4.4.0 urllib3: 1.26.12 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 zipp: 3.10.0 File attachment: out_15898.pdb }}} [attachment:""out_15898.pdb""] " defect closed normal Structure Analysis not a bug all ChimeraX