id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4500 glUniformMatrix4fv: invalid operation chimerax-bug-report@… Tom Goddard "{{{ 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 (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. How to cite UCSF ChimeraX > open C:\Users\adamw\Downloads\6vyb.pdb format pdb 6vyb.pdb title: Sars-cov-2 spike ectodomain structure (open state) [more info...] Chain information for 6vyb.pdb #1 --- Chain | Description A B C | spike glycoprotein Non-standard residues in 6vyb.pdb #1 --- NAG — 2-acetamido-2-deoxy-β-D-glucopyranose > ui tool show ""Basic Actions"" Alignment identifier is 1 > set bgColor white > lighting simple > lighting soft > lighting full > lighting simple > set bgColor gray > lighting simple > set bgColor white > view > view > view > ui tool show ""Basic Actions"" > view > ui tool show ""Basic Actions"" Alignment identifier is 1 > style sphere Changed 22365 atom styles > color bychain > color byhetero > color bychain > color byhetero > select /A 7533 atoms, 7716 bonds, 24 pseudobonds, 976 residues, 2 models selected > select /A 7533 atoms, 7716 bonds, 24 pseudobonds, 976 residues, 2 models selected Alignment identifier is 1/A > view > view > view > view > view sel > view > view sel > view > view sel > hide sel atoms > hide sel surfaces > style sel stick Changed 89 atom styles > style sel ball Changed 89 atom styles > view > view sel > view > view > view > view > view sel > close session > open C:/Users/adamw/Downloads/6vsb.pdb 6vsb.pdb title: Prefusion 2019-ncov spike glycoprotein with A single receptor-binding domain up [more info...] Chain information for 6vsb.pdb #1 --- Chain | Description A B C | spike glycoprotein Non-standard residues in 6vsb.pdb #1 --- NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine; 2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine) > ui tool show ""Basic Actions"" > select /A 7437 atoms, 7614 bonds, 26 pseudobonds, 968 residues, 2 models selected Alignment identifier is 1/A > view sel > close session > open C:/Users/adamw/Downloads/6vge.pdb 6vge.pdb title: Crystal structure of the DNA binding domains of human transcription factor erg, human RUNX2 bound to core binding factor β (CBFB), In complex with 16MER DNA cagaggatgtggcttc [more info...] Chain information for 6vge.pdb #1 --- Chain | Description A | transforming protein ERG B | DNA (5'- D(P*CP*ap*GP*ap*GP*GP*ap*TP*GP*TP*GP*GP*CP*TP*TP*C)-3') C | DNA (5'- D(P*GP*ap*ap*GP*CP*CP*ap*CP*ap*TP*CP*CP*TP*CP*TP*G)-3') D | runt-related transcription factor 2 G | core-binding factor subunit β > ui tool show ""Basic Actions"" 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 ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\core\updateloop.py"", line 73, in draw_new_frame view.draw(check_for_changes = False) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\graphics\view.py"", line 165, in draw self._draw_scene(camera, drawings) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\graphics\view.py"", line 229, in _draw_scene draw_depth(r, opaque_drawings) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\graphics\drawing.py"", line 1510, in draw_depth draw_opaque(r, drawings) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\graphics\drawing.py"", line 1486, in draw_opaque _draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\graphics\drawing.py"", line 1499, in _draw_multiple d.draw(renderer, draw_pass) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\graphics\drawing.py"", line 739, in draw self.draw_self(renderer, draw_pass) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\graphics\drawing.py"", line 746, in draw_self self._draw_geometry(renderer, opaque_only = any_transp) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\graphics\drawing.py"", line 777, in _draw_geometry shader = r.shader(sopt) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\graphics\opengl.py"", line 588, in shader p = self._opengl_shader(options) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\graphics\opengl.py"", line 691, in _opengl_shader self._use_shader(p) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\graphics\opengl.py"", line 615, in _use_shader self.set_projection_matrix() File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\graphics\opengl.py"", line 707, in set_projection_matrix p.set_matrix('projection_matrix', pm) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\graphics\opengl.py"", line 2688, in set_matrix GL.glUniformMatrix4fv(self.uniform_id(name), 1, False, matrix) File ""src\latebind.pyx"", line 39, in OpenGL_accelerate.latebind.LateBind.__call__ File ""src\wrapper.pyx"", line 318, in OpenGL_accelerate.wrapper.Wrapper.__call__ File ""src\wrapper.pyx"", line 311, in OpenGL_accelerate.wrapper.Wrapper.__call__ File ""src\errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1282, description = b'invalid operation', baseOperation = glUniformMatrix4fv, pyArgs = ( 1, 1, False, , ), cArgs = ( 1, 1, False, , ), cArguments = ( 1, 1, False, , ) ) OpenGL version: 3.3.13596 Core Profile Forward-Compatible Context 20.10.40 27.20.11040.11 OpenGL renderer: AMD Radeon(TM) Vega 8 Graphics OpenGL vendor: ATI Technologies Inc. Manufacturer: HP Model: HP All-in-One 24-dp0xxx OS: Microsoft Windows 10 Home (Build 19041) Memory: 10,650,955,776 MaxProcessMemory: 137,438,953,344 CPU: 8 AMD Ryzen 5 3500U with Radeon Vega Mobile Gfx "" 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: 2.1.1 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-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: 1.0 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.0 ChimeraX-IMOD: 1.0 ChimeraX-IO: 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 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 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 Graphics can't reproduce all ChimeraX