id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6195 Attempt to retrieve context when no valid context sabarik@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Linux-5.10.0-1057-oem-x86_64-with-glibc2.14 ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC) Description Added a bond distance to a metalloprotein active site model. Log: UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Thank you for registering your copy of ChimeraX. By providing the information requested you will be helping us document the impact this software is having in the scientific community. The information you supplied will only be used for reporting summary usage statistics; no individual data will be released. sabarik@colostate.edu is subscribed to the ChimeraX discussion list sabarik@colostate.edu is subscribed to the ChimeraX announcements list > ui tool show ""Build Structure"" > ui tool show ""Basic Actions"" > open > /home/sabari/Documents/College/GradSchool/CSU/Coursework/CHEM578AComputationalChemistry/GH61/Step3/GH61_Active_Step3_Ch1_Singlet.log Opened GH61_Active_Step3_Ch1_Singlet.log as a Gaussian output file > ui tool show Distances > select add /a:1@N1 1 atom, 1 residue, 1 model selected > select add /a:1@Cu1 2 atoms, 1 residue, 1 model selected > distance /a:1@N1 /a:1@Cu1 Distance between /a UNK 1 N1 and Cu1: 1.893Å > select add /a:1@N5 3 atoms, 1 residue, 1 model selected > select clear > select /a:1@N5 1 atom, 1 residue, 1 model selected > select add /a:1@Cu1 2 atoms, 1 residue, 1 model selected > distance /a:1@N5 /a:1@Cu1 Distance between /a UNK 1 N5 and Cu1: 1.901Å > select clear > select /a:1@Cu1 1 atom, 1 residue, 1 model selected > select add /a:1@O4 2 atoms, 1 residue, 1 model selected > distance /a:1@Cu1 /a:1@O4 Distance between /a UNK 1 Cu1 and O4: 1.985Å > select clear > select /a:1@Cu1 1 atom, 1 residue, 1 model selected > select add /a:1@N2 2 atoms, 1 residue, 1 model selected > distance /a:1@Cu1 /a:1@N2 Distance between /a UNK 1 Cu1 and N2: 1.887Å An error occurred in drawing the scene. Redrawing graphics is now stopped to avoid a continuous stream of error messages. To restart graphics use the command ""graphics restart"" after changing the settings that caused the error. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/core/updateloop.py"", line 73, in draw_new_frame view.draw(check_for_changes = False) File ""/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/graphics/view.py"", line 165, in draw self._draw_scene(camera, drawings) File ""/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/graphics/view.py"", line 250, in _draw_scene draw_on_top(r, on_top_drawings) File ""/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/graphics/drawing.py"", line 1575, in draw_on_top _draw_multiple(drawings, renderer, Drawing.LAST_DRAW_PASS) File ""/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/graphics/drawing.py"", line 1511, in _draw_multiple d.draw(renderer, draw_pass) File ""/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/graphics/drawing.py"", line 751, in draw self.draw_self(renderer, draw_pass) File ""/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/graphics/drawing.py"", line 767, in draw_self self._draw_geometry(renderer) File ""/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/graphics/drawing.py"", line 785, in _draw_geometry ds.activate_bindings(renderer) File ""/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/graphics/drawing.py"", line 1858, in activate_bindings self.update_buffers() File ""/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/graphics/drawing.py"", line 1848, in update_buffers bi.bind_shader_variable(b) File ""/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/graphics/opengl.py"", line 2486, in bind_shader_variable GL.glVertexAttribPointer(attr_id, ncomp, gtype, normalize, 0, None) File ""src/latebind.pyx"", line 51, in OpenGL_accelerate.latebind.Curry.__call__ File ""/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/OpenGL/GL/VERSION/GL_2_0.py"", line 469, in glVertexAttribPointer contextdata.setValue( key, array ) File ""/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/OpenGL/contextdata.py"", line 58, in setValue context = getContext( context ) File ""/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/OpenGL/contextdata.py"", line 40, in getContext raise error.Error( OpenGL.error.Error: Attempt to retrieve context when no valid context OpenGL version: 3.3.0 NVIDIA 510.47.03 OpenGL renderer: NVIDIA GeForce GTX 1650 Ti with Max-Q Design/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: LENOVO Model: 20TK001EUS OS: Ubuntu 20.04 focal Architecture: 64bit ELF Virutal Machine: none CPU: 12 Intel(R) Core(TM) i7-10750H CPU @ 2.60GHz Cache Size: 12288 KB Memory: total used free shared buff/cache available Mem: 23Gi 12Gi 524Mi 437Mi 10Gi 10Gi Swap: 2.0Gi 44Mi 2.0Gi Graphics: 00:02.0 VGA compatible controller [0300]: Intel Corporation UHD Graphics [8086:9bc4] (rev 05) Subsystem: Lenovo Device [17aa:22c0] Kernel driver in use: i915 Locale: ('en_US', 'UTF-8') 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: 2020.12.5 cftime: 1.5.0 chardet: 3.0.4 ChimeraX-AddCharge: 1.0.1 ChimeraX-AddH: 2.1.3 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.13.2 ChimeraX-AtomicLibrary: 3.1.3 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.5.2 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1 ChimeraX-Clipper: 0.16.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.2.1 ChimeraX-CommandLine: 1.1.4 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2.5 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.1.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.3 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: 2.1 ChimeraX-Help: 1.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.2.2 ChimeraX-Label: 1.0 ChimeraX-LinuxSupport: 1.0 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.0.2 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: 1.2.1 ChimeraX-MDcrds: 2.2 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.3 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.0.1 ChimeraX-ModelPanel: 1.0.1 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: 2.0.1 ChimeraX-OpenCommand: 1.5 ChimeraX-PDB: 2.4.1 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.1 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.0.1 ChimeraX-ReadPbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.4 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.3 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: 2.0.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.3.1 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: 1.0.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.7.6 ChimeraX-uniprot: 2.1 ChimeraX-UnitCell: 1.0 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: 0.29.21 decorator: 5.0.9 distlib: 0.3.1 distro: 1.5.0 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.17 imagecodecs: 2020.5.30 imagesize: 1.2.0 ipykernel: 5.3.4 ipython: 7.18.1 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.7 jupyter-core: 4.7.1 kiwisolver: 1.3.1 line-profiler: 2.1.2 lxml: 4.6.2 lz4: 3.1.0 MarkupSafe: 2.0.1 matplotlib: 3.3.2 msgpack: 1.0.0 netCDF4: 1.5.4 networkx: 2.5 numexpr: 2.7.3 numpy: 1.19.2 numpydoc: 1.1.0 openvr: 1.14.1501 packaging: 20.9 ParmEd: 3.2.0 parso: 0.7.1 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 7.2.0 pip: 21.0.1 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.18 psutil: 5.7.2 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.7.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.1 pytz: 2021.1 pyzmq: 22.0.3 qtconsole: 4.7.7 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.5.2 Send2Trash: 1.8.0 SEQCROW: 1.3 setuptools: 50.3.2 sfftk-rw: 0.6.7.dev1 six: 1.15.0 snowballstemmer: 2.1.0 sortedcontainers: 2.2.2 Sphinx: 3.2.1 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: 2020.9.3 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.0 wheel-filename: 1.2.0 }}} " defect closed normal Graphics can't reproduce Greg Couch tony.schaefer@… all ChimeraX