id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4191 Coulombic failure due to unexpected hydrogen name cesar.menor@… 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 Trying to color surface by electrostatic potential (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. > open ""J:\My Stuff\BIOQUIMICA\Estructuras PDB\ribosoma.cxs"" format session Log from Fri Jan 15 23:03:03 2021UCSF ChimeraX version: 1.1 (2020-09-09) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""J:/My Stuff/BIOQUIMICA/Estructuras PDB/4v4i modified.pdb"" Summary of feedback from opening J:/My Stuff/BIOQUIMICA/Estructuras PDB/4v4i modified.pdb --- warnings | Ignored bad PDB record found on line 6465 END Start residue of secondary structure not found: HELIX 1 1 ARG A 9 GLU A 13 1 5 Start residue of secondary structure not found: HELIX 2 2 GLU A 25 LEU A 33 1 9 Start residue of secondary structure not found: HELIX 3 3 SER A 55 GLN A 57 1 3 Start residue of secondary structure not found: HELIX 4 4 PRO A 183 ALA A 187 1 5 Start residue of secondary structure not found: HELIX 5 5 ARG A 191 GLU A 198 1 8 240 messages similar to the above omitted CONECT record for nonexistent atom: 6901 Start residue of secondary structure not found: HELIX 1 1 ARG A 9 GLU A 13 1 5 Start residue of secondary structure not found: HELIX 2 2 GLU A 25 LEU A 33 1 9 Start residue of secondary structure not found: HELIX 3 3 SER A 55 GLN A 57 1 3 Start residue of secondary structure not found: HELIX 4 4 PRO A 183 ALA A 187 1 5 Start residue of secondary structure not found: HELIX 5 5 ARG A 191 GLU A 198 1 8 240 messages similar to the above omitted Chain information for 4v4i modified.pdb --- Chain | Description 1.1/0 | No description available 1.1/1 | No description available 1.2/Y | No description available 1.2/x | No description available 1.1/z | No description available > select #1.2/x 560 atoms, 615 bonds, 28 residues, 1 model selected > select #1.1/z 1628 atoms, 1818 bonds, 76 residues, 1 model selected > select #1.1/0 1621 atoms, 1813 bonds, 76 residues, 1 model selected > close session > open ""J:/My Stuff/BIOQUIMICA/Estructuras PDB/4v4i modified2.pdb"" Summary of feedback from opening J:/My Stuff/BIOQUIMICA/Estructuras PDB/4v4i modified2.pdb --- warnings | Ignored bad PDB record found on line 160213 END Start residue of secondary structure not found: HELIX 1 1 ARG A 9 GLU A 13 1 5 Start residue of secondary structure not found: HELIX 2 2 GLU A 25 LEU A 33 1 9 Start residue of secondary structure not found: HELIX 3 3 SER A 55 GLN A 57 1 3 Start residue of secondary structure not found: HELIX 4 4 PRO A 183 ALA A 187 1 5 Start residue of secondary structure not found: HELIX 5 5 ARG A 191 GLU A 198 1 8 240 messages similar to the above omitted Chain information for 4v4i modified2.pdb --- Chain | Description 1.1/0 | No description available 1.1/1 | No description available 1.2/1 | No description available 1.2/2 | No description available 1.1/A | No description available 1.2/A | No description available 1.1/B | No description available 1.1/C | No description available 1.1/D | No description available 1.1/E | No description available 1.1/F | No description available 1.1/G | No description available 1.1/H | No description available 1.1/I | No description available 1.1/J | No description available 1.1/K | No description available 1.1/L | No description available 1.1/M | No description available 1.1/N | No description available 1.1/O | No description available 1.1/P | No description available 1.1/Q | No description available 1.1/R | No description available 1.1/S | No description available 1.1/T | No description available 1.1/U | No description available 1.1/V | No description available 1.1/W | No description available 1.1/X | No description available 1.2/X | No description available 1.1/Y | No description available 1.2/Y | No description available 1.1/Z | No description available 1.1/a | No description available 1.2/a | No description available 1.1/b | No description available 1.2/b | No description available 1.1/c | No description available 1.2/c | No description available 1.1/d | No description available 1.1/e | No description available 1.1/f | No description available 1.1/g | No description available 1.1/h | No description available 1.1/i | No description available 1.1/j | No description available 1.1/k | No description available 1.1/l | No description available 1.1/m | No description available 1.1/n | No description available 1.1/o | No description available 1.1/p | No description available 1.1/q | No description available 1.1/r | No description available 1.1/s | No description available 1.1/t | No description available 1.1/u | No description available 1.1/v | No description available 1.1/w | No description available 1.1/x | No description available 1.2/x | No description available 1.1/y | No description available 1.1/z | No description available > select #1.1/0 1621 atoms, 1813 bonds, 76 residues, 1 model selected > select add #1.1/1 1743 atoms, 1948 bonds, 82 residues, 1 model selected > select add #1.1/Z 2161 atoms, 2374 bonds, 130 residues, 1 model selected > select add #1.1/m 3131 atoms, 3360 bonds, 254 residues, 1 model selected > select add #1.1/n 4128 atoms, 4368 bonds, 379 residues, 1 model selected > select add #1.1/Y 4564 atoms, 4817 bonds, 435 residues, 1 model selected > select ~sel 154238 atoms, 167793 bonds, 2 pseudobonds, 10957 residues, 4 models selected > hide (#1.2#!1.1 & sel) target a > select clear > select add #1.1/1#1.2/1 3012 atoms, 3367 bonds, 141 residues, 2 models selected > cartoon sel > cartoon hide sel > select add #1.1/1 3012 atoms, 3367 bonds, 141 residues, 2 models selected > cartoon sel > select add #1.1/Z 3430 atoms, 3793 bonds, 189 residues, 2 models selected > cartoon hide sel > hide sel target a > select add #1.1/0 5051 atoms, 5606 bonds, 265 residues, 2 models selected > select add #1.1/z 6679 atoms, 7424 bonds, 341 residues, 2 models selected > cartoon sel > select clear > select add #1.1/1 122 atoms, 135 bonds, 6 residues, 1 model selected > cartoon sel > surface sel > select add #1.1/Y 558 atoms, 584 bonds, 62 residues, 2 models selected > select #1.2/Y 1647 atoms, 1840 bonds, 77 residues, 1 model selected > cartoon sel > select #1.1/x 2573 atoms, 2878 bonds, 120 residues, 1 model selected > cartoon sel > cartoon hide sel > select #1.2/x 560 atoms, 615 bonds, 28 residues, 1 model selected > cartoon sel > surface sel > select #1.1/0 1621 atoms, 1813 bonds, 76 residues, 1 model selected > surface sel > select #1.1/z 1628 atoms, 1818 bonds, 76 residues, 1 model selected > surface sel > select #1.1/n 997 atoms, 1008 bonds, 125 residues, 1 model selected > surface sel > set bgColor white > select #1.2/Y 1647 atoms, 1840 bonds, 77 residues, 1 model selected > surface sel > select #1.1/Y 436 atoms, 449 bonds, 56 residues, 1 model selected > hide sel target a > select #1.1/Z 418 atoms, 426 bonds, 48 residues, 1 model selected > cartoon hide sel > select #1.1/m 970 atoms, 986 bonds, 124 residues, 1 model selected > surface sel > select clear > save ""J:/My Stuff/BIOQUIMICA/Estructuras PDB/ribosoma.cxs"" opened ChimeraX session > select #1.2/2 1057 atoms, 1177 bonds, 50 residues, 1 model selected > show sel cartoons > hide sel cartoons > select #1.2/A 3272 atoms, 3346 bonds, 427 residues, 1 model selected > show sel cartoons > coulombic sel The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics: 4v4i modified2.pdb #1.2/A LYS 164 CG, 4v4i modified2.pdb #1.2/A LYS 164 CE, 4v4i modified2.pdb #1.2/A LYS 164 CD, 4v4i modified2.pdb #1.2/A LYS 164 NZ, 4v4i modified2.pdb #1.2/A LYS 39 CG, and 74 other atoms copy of 4v4i modified2.pdb #/A SER 337 HB Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\toolbar\tool.py"", line 202, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\core\toolshed\info.py"", line 363, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 1273, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\shortcuts\\__init__.py"", line 52, in run_provider shortcuts.run_provider(session, name) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 1221, in run_provider keyboard_shortcuts(session).try_shortcut(name) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 376, in try_shortcut self.run_shortcut(keys) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 394, in run_shortcut sc.run(self.session, status = self._enabled) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 313, in run f(s) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 537, in run_expanded_command run(session, cmd) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 480, in run run_command(session, command, **kw) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\core\commands\run.py"", line 31, in run results = command.run(text, log=log) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\coulombic\cmd.py"", line 97, in cmd_coulombic assign_charges(session, needs_assignment, his_scheme) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\coulombic\coulombic.py"", line 96, in assign_charges assign_residue_charges(charged_residues, his_scheme) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\coulombic\coulombic.py"", line 161, in assign_residue_charges a.charge = res_data[aname] KeyError: 'HB' KeyError: 'HB' File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\coulombic\coulombic.py"", line 161, in assign_residue_charges a.charge = res_data[aname] See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 460.89 OpenGL renderer: GeForce GTX 960/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: MICRO-STAR INTERNATIONAL CO., LTD Model: MS-B08911 OS: Microsoft Windows 10 Home (Build 19041) Memory: 8,514,162,688 MaxProcessMemory: 137,438,953,344 CPU: 4 Intel(R) Core(TM) i5-4460S CPU @ 2.90GHz"" 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-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-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-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 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 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 Send2Trash: 1.5.0 SEQCROW: 0.24b0 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 stripy: 2.0.2 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 }}} " defect closed normal Surface/Binding Analysis fixed all ChimeraX