id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6158 Open BILD file: float division by zero venkatareddy@… Greg Couch "{{{ The following bug report has been submitted: Platform: Linux-5.13.0-28-generic-x86_64-with-glibc2.31 ChimeraX Version: 1.3rc202111230539 (2021-11-23 05:39:18 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.3rc202111230539 (2021-11-23) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 6nj9_NCP_K79NZ_ori_cen_onY.pdb Summary of feedback from opening 6nj9_NCP_K79NZ_ori_cen_onY.pdb --- warnings | Ignored bad PDB record found on line 629 Ignored bad PDB record found on line 1474 Ignored bad PDB record found on line 2219 Ignored bad PDB record found on line 3038 Ignored bad PDB record found on line 3857 5 messages similar to the above omitted Duplicate atom serial number found: 2138 Chain information for 6nj9_NCP_K79NZ_ori_cen_onY.pdb #1 --- Chain | Description A E | No description available B F | No description available C G | No description available D H | No description available I | No description available J | No description available > open MT67_rxn_ori_cen_onY.pdb Chain information for MT67_rxn_ori_cen_onY.pdb #2 --- Chain | Description A | No description available B | No description available > select clear > select #2/B:412@CE 1 atom, 1 residue, 1 model selected > select up 27 atoms, 29 bonds, 1 residue, 1 model selected > open > /home/venkatareddy/workspace/analysis_mcqeen_14062021/Rv2067c/paper_Rv2067c/Rv2067c_NCP_hypothesis/pdb_transformations_and_ProteinEuler/xyz_axes.bild Opened BILD data containing 6 objects > open > /home/venkatareddy/workspace/analysis_mcqeen_14062021/Rv2067c/paper_Rv2067c/Rv2067c_NCP_hypothesis/pdb_transformations_and_ProteinEuler/xyz_axes.bild Opened BILD data containing 6 objects > close #4 > close #3 > open > /home/venkatareddy/workspace/analysis_mcqeen_14062021/Rv2067c/paper_Rv2067c/Rv2067c_NCP_hypothesis/pdb_transformations_and_ProteinEuler/XYZ- > axes.bild Opened BILD data containing 4 objects > close #3 > open > /home/venkatareddy/workspace/analysis_mcqeen_14062021/Rv2067c/paper_Rv2067c/Rv2067c_NCP_hypothesis/pdb_transformations_and_ProteinEuler/xyz_axes.bild Opened BILD data containing 6 objects > select #1/J:98@OP1 1 atom, 1 residue, 1 model selected > getcrd sel Atom #1/J:98@OP1 33.189 3.409 7.190 > select #1/I:43@C5' 1 atom, 1 residue, 1 model selected > select clear Drag select of 1 atoms > select clear > select #1/J:99@OP1 1 atom, 1 residue, 1 model selected > getcrd sel Atom #1/J:99@OP1 26.155 4.604 8.275 > select #2/B:188 9 atoms, 8 bonds, 1 residue, 1 model selected > getcrd sel Atom #2/B:188@N 12.643 3.639 13.872 Atom #2/B:188@CA 12.744 4.542 15.036 Atom #2/B:188@CB 13.831 3.960 15.938 Atom #2/B:188@CG 14.282 4.787 17.115 Atom #2/B:188@CD 15.432 4.081 17.803 Atom #2/B:188@CE 15.385 4.096 19.317 Atom #2/B:188@NZ 15.688 5.455 19.797 Atom #2/B:188@C 12.989 5.980 14.563 Atom #2/B:188@O 12.287 6.864 15.038 > select clear > hide atoms > show cartoons > select clear > select #1/e:79 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 9 atom styles > color sel byhetero > select clear > select :sam 54 atoms, 58 bonds, 2 residues, 1 model selected > show sel atoms > style sel sphere Changed 54 atom styles > select clear > set bgColor white > select #1 & nucleicacid Expected a keyword > select #1 & nucleic 5986 atoms, 6714 bonds, 292 residues, 1 model selected > ui tool show ""Color Actions"" [Repeated 2 time(s)] > color sel dim gray > select clear > select #1 & protein 6060 atoms, 6140 bonds, 764 residues, 1 model selected > color sel silver > select clear > select #2 6251 atoms, 6424 bonds, 782 residues, 1 model selected > color sel dark cyan [Repeated 1 time(s)] > lighting soft > color sel dodger blue > color sel cornflower blue > color sel hot pink > color sel dodger blue > color sel cornflower blue > hide #1 models > select clear > select #2/B:412@CE 1 atom, 1 residue, 1 model selected > select up 27 atoms, 29 bonds, 1 residue, 1 model selected > style sel stick Changed 27 atom styles > select clear > hide #3 models > select @h Nothing selected > select clear > show #2 atoms > hide #2 atoms > select :sam 54 atoms, 58 bonds, 2 residues, 1 model selected > show sel atoms > select clear > select :dum 3 atoms, 3 residues, 2 models selected > show sel & #2 atoms > select clear > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > show #3 models > hide #3 models > select #2/Z:413@HG 1 atom, 1 residue, 1 model selected > cofr sel > select clear > select #2/B:412@CE 1 atom, 1 residue, 1 model selected > select add #2/B:412@SD 2 atoms, 1 residue, 1 model selected > select #2/Z:413@HG 1 atom, 1 residue, 1 model selected > select clear > select #2/Z:413@HG 1 atom, 1 residue, 1 model selected > select add #2/B:412@CE 2 atoms, 2 residues, 1 model selected > select add #2/B:412@SD 3 atoms, 2 residues, 1 model selected > style sel ball Changed 3 atom styles > select clear > show #3 models > turn x 10 models #2 [Repeated 7 time(s)] > open > /home/venkatareddy/workspace/analysis_mcqeen_14062021/Rv2067c/paper_Rv2067c/Rv2067c_NCP_hypothesis/pdb_transformations_and_ProteinEuler/xyz_axes.bild Opened BILD data containing 6 objects > hide #3 models > open > /home/venkatareddy/workspace/analysis_mcqeen_14062021/Rv2067c/paper_Rv2067c/Rv2067c_NCP_hypothesis/pdb_transformations_and_ProteinEuler/xyz_axes.bild > format bild Summary of feedback from opening /home/venkatareddy/workspace/analysis_mcqeen_14062021/Rv2067c/paper_Rv2067c/Rv2067c_NCP_hypothesis/pdb_transformations_and_ProteinEuler/xyz_axes.bild --- warnings | Expected 'x1 y1 z1 x2 y2 z2' after .vector on line 4 Expected 'x1 y1 z1 x2 y2 z2' after .vector on line 8 Expected 'x1 y1 z1 x2 y2 z2' after .vector on line 12 Opened BILD data containing 3 objects > hide #4 models > open > /home/venkatareddy/workspace/analysis_mcqeen_14062021/Rv2067c/paper_Rv2067c/Rv2067c_NCP_hypothesis/pdb_transformations_and_ProteinEuler/xyz_axes.bild > format bild Opened BILD data containing 6 objects > close #3-6 > open > /home/venkatareddy/workspace/analysis_mcqeen_14062021/Rv2067c/paper_Rv2067c/Rv2067c_NCP_hypothesis/pdb_transformations_and_ProteinEuler/xyz_axes.bild > format bild Summary of feedback from opening /home/venkatareddy/workspace/analysis_mcqeen_14062021/Rv2067c/paper_Rv2067c/Rv2067c_NCP_hypothesis/pdb_transformations_and_ProteinEuler/xyz_axes.bild --- warnings | Expected 'x1 y1 z1 x2 y2 z2' after .vector on line 4 Expected 'x1 y1 z1 x2 y2 z2' after .vector on line 8 Expected 'x1 y1 z1 x2 y2 z2' after .vector on line 12 Opened BILD data containing 3 objects > open > /home/venkatareddy/workspace/analysis_mcqeen_14062021/Rv2067c/paper_Rv2067c/Rv2067c_NCP_hypothesis/pdb_transformations_and_ProteinEuler/XYZ- > axes.bild format bild Opened BILD data containing 4 objects > close #4 > open > /home/venkatareddy/workspace/analysis_mcqeen_14062021/Rv2067c/paper_Rv2067c/Rv2067c_NCP_hypothesis/pdb_transformations_and_ProteinEuler/xyz_axes.bild Summary of feedback from opening /home/venkatareddy/workspace/analysis_mcqeen_14062021/Rv2067c/paper_Rv2067c/Rv2067c_NCP_hypothesis/pdb_transformations_and_ProteinEuler/xyz_axes.bild --- warnings | Expected 'x1 y1 z1 x2 y2 z2' after .vector on line 4 Expected 'x1 y1 z1 x2 y2 z2' after .vector on line 8 Expected 'x1 y1 z1 x2 y2 z2' after .vector on line 12 Opened BILD data containing 3 objects > hide #3 models > hide #4 models > show #4 models > close #3-4 > open > /home/venkatareddy/workspace/analysis_mcqeen_14062021/Rv2067c/paper_Rv2067c/Rv2067c_NCP_hypothesis/pdb_transformations_and_ProteinEuler/xyz_axes.bild > format bild Opened BILD data containing 6 objects > open > /home/venkatareddy/workspace/analysis_mcqeen_14062021/Rv2067c/paper_Rv2067c/Rv2067c_NCP_hypothesis/pdb_transformations_and_ProteinEuler/xyz_axes.bild > format bild Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 333, in interceptRequest self._callback(info) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 92, in _intercept return interceptor(request_info, *args) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 366, in intercept chimerax_intercept(*args, view=view, session=session) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 468, in chimerax_intercept session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 382, in thread_safe func(*args, **kw) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 459, in defer cxcmd(session, topic) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 477, in cxcmd run(session, cmd) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 181, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 432, in collated_open return remember_data_format() File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 403, in remember_data_format models, status = func(*func_args, **func_kw) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/bild/__init__.py"", line 34, in open return bild.read_bild(session, data, file_name) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/bild/bild.py"", line 589, in read_bild return b.parse_stream(stream) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/bild/bild.py"", line 111, in parse_stream func(self, tokens) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/bild/bild.py"", line 153, in arrow_command vertices2, normals2, triangles2 = get_cone( File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/bild/bild.py"", line 646, in get_cone vertices, normals, triangles = surface.cone_geometry(radius, height=h, caps=bottom) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/surface/shapes.py"", line 182, in cone_geometry znorm = radius/height if points_up else -radius/height ZeroDivisionError: float division by zero ZeroDivisionError: float division by zero File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/surface/shapes.py"", line 182, in cone_geometry znorm = radius/height if points_up else -radius/height See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 470.103.01 OpenGL renderer: NVIDIA GeForce GTX 1050 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Model: OS: Ubuntu 20.04 focal Architecture: 64bit ELF Virutal Machine: none CPU: 8 Intel(R) Core(TM) i7-3770 CPU @ 3.40GHz Cache Size: 8192 KB Memory: total used free shared buff/cache available Mem: 15Gi 9.2Gi 3.5Gi 262Mi 2.8Gi 5.8Gi Swap: 15Gi 3.6Gi 11Gi Graphics: 01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP107 [GeForce GTX 1050 Ti] [10de:1c82] (rev a1) Subsystem: Gigabyte Technology Co., Ltd GP107 [GeForce GTX 1050 Ti] [1458:3764] Kernel driver in use: nvidia Locale: ('en_IN', 'ISO8859-1') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.10.8 cftime: 1.5.1.1 charset-normalizer: 2.0.7 ChimeraX-AddCharge: 1.2.1 ChimeraX-AddH: 2.1.10 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.30.2 ChimeraX-AtomicLibrary: 4.1.5 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6 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 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3rc202111230539 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-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: 1.1 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-LinuxSupport: 1.0 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 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: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 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: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 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: 2.4.6 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: 1.6.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13.7 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 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: 0.29.24 decorator: 5.1.0 distro: 1.6.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 line-profiler: 3.3.0 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 MolecularDynamicsViewer: 1.2 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.7.3 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.3 ParmEd: 3.2.0 parso: 0.8.2 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.22 psutil: 5.8.0 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.2 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 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-jurko: 0.6 tables: 3.6.1 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 }}} " defect closed normal Input/Output fixed all ChimeraX