id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8577 glDrawBuffer: invalid operation chimerax-bug-report@… Tom Goddard "The following bug report has been submitted: Platform: Linux-5.15.0-58-generic-x86_64-with-glibc2.35 ChimeraX Version: 1.6.dev202301280224 (2023-01-28 02:24:25 UTC) Description (Describe the actions that caused this problem to occur here) Log: Startup Errors --- error | Bundle 'ChimeraX-ISOLDE' custom initialization failed warning | Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 490, in get_module m = importlib.import_module(self.package_name) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/importlib/__init__.py"", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File """", line 1030, in _gcd_import File """", line 1007, in _find_and_load File """", line 986, in _find_and_load_unlocked File """", line 680, in _load_unlocked File """", line 850, in exec_module File """", line 228, in _call_with_frames_removed File ""/home/mnakasone/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/__init__.py"", line 51, in __version__ = _version() File ""/home/mnakasone/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/__init__.py"", line 49, in _version return pkg_resources.require('ChimeraX-ISOLDE')[0].version File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site- packages/pkg_resources/__init__.py"", line 909, in require needed = self.resolve(parse_requirements(requirements)) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site- packages/pkg_resources/__init__.py"", line 795, in resolve raise DistributionNotFound(req, requirers) pkg_resources.DistributionNotFound: The 'ChimeraX-Clipper~=0.20.0' distribution was not found and is required by ChimeraX-ISOLDE During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 364, in initialize api = self._get_api(session.logger) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 509, in _get_api m = self.get_module() File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 492, in get_module raise ToolshedError(""Error importing bundle %s's module: %s"" % (self.name, str(e))) chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's module: The 'ChimeraX-Clipper~=0.20.0' distribution was not found and is required by ChimeraX-ISOLDE UCSF ChimeraX version: 1.6.dev202301280224 (2023-01-28) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX open /home/mnakasone/Downloads/cryosparc_P4_J227_map_sharp.mrc Opened cryosparc_P4_J227_map_sharp.mrc as #1, grid size 256,256,256, pixel 0.867, shown at level 0.0273, step 1, values float32 volume #1 level 0.01171 open ""/home/mnakasone/Downloads/cryosparc_P4_J272_class_00_00102_volume_sharp (2).mrc"" Opened cryosparc_P4_J272_class_00_00102_volume_sharp (2).mrc as #2, grid size 256,256,256, pixel 0.867, shown at level 0.0297, step 1, values float32 volume #2 level 0.02239 volume #1 color #1a5fb4 set bgColor white volume #1 color #241f31 volume #1 color #1a5fb4 volume #2 color #c01c28 volume #2 color #e5a50a volume #2 color #f5c211 vop morph volume morph Missing or invalid ""volumes"" argument: empty atom specifier select add #1 2 models selected select add #2 4 models selected vop morph volume morph Missing or invalid ""volumes"" argument: empty atom specifier ui tool show ""Volume Viewer"" vop morph volume morph Missing or invalid ""volumes"" argument: empty atom specifier morph Missing or invalid ""structures"" argument: empty atom specifier volume morph Missing or invalid ""volumes"" argument: empty atom specifier volume morph #1-10 Opened morph as #3, grid size 256,256,256, pixel 0.867, shown at step 1, values float32 volume morph #1-10 Opened morph as #4, grid size 256,256,256, pixel 0.867, shown at step 1, values float32 volume morph #1-10 Opened morph as #5, grid size 256,256,256, pixel 0.867, shown at step 1, values float32 volume morph #1-10 Opened morph as #6, grid size 256,256,256, pixel 0.867, shown at step 1, values float32 volume morph #1-10 Opened morph as #7, grid size 256,256,256, pixel 0.867, shown at step 1, values float32 volume #2 level 0.03344 volume #3 level 0.02168 volume morph #1-10 Opened morph as #8, grid size 256,256,256, pixel 0.867, shown at step 1, values float32 volume morph #1-10 Opened morph as #9, grid size 256,256,256, pixel 0.867, shown at step 1, values float32 volume #9 level 0.02062 volume #8 level 0.02133 volume #7 level 0.02133 volume #6 level 0.01955 volume morph #1-10 Opened morph as #10, grid size 256,256,256, pixel 0.867, shown at step 1, values float32 volume #10 level 0.02097 volume morph #1-10 Opened morph as #11, grid size 256,256,256, pixel 0.867, shown at step 1, values float32 volume #11 level 0.02133 volume morph #1-2 Opened morph as #12, grid size 256,256,256, pixel 0.867, shown at step 1, values float32 volume morph #1-2 Opened morph as #13, grid size 256,256,256, pixel 0.867, shown at step 1, values float32 volume morph #1-2 Opened morph as #14, grid size 256,256,256, pixel 0.867, shown at step 1, values float32 volume #3 level 0.02879 volume #5 level 0.0281 close #3 close #7 close #9 close #5-6,8,10-14 close #4 show #!1 models show #!2 models fitmap #1 inMap #2 Fit map cryosparc_P4_J227_map_sharp.mrc in map cryosparc_P4_J272_class_00_00102_volume_sharp (2).mrc using 388280 points correlation = 0.9307, correlation about mean = 0.7558, overlap = 436.8 steps = 112, shift = 9.71, angle = 4.03 degrees Position of cryosparc_P4_J227_map_sharp.mrc (#1) relative to cryosparc_P4_J272_class_00_00102_volume_sharp (2).mrc (#2) coordinates: Matrix rotation and translation 0.99820078 -0.02060691 -0.05630774 7.54006188 0.02266490 0.99908903 0.03615818 -6.08346442 0.05551133 -0.03736933 0.99775850 -11.28560744 Axis -0.52277164 -0.79501999 0.30765731 Axis point 193.21001995 -0.00000000 103.80574150 Rotation angle (degrees) 4.03263666 Shift along axis -2.57735437 volume morph #1-2 Map positions are not the same, cryosparc_P4_J272_class_00_00102_volume_sharp (2).mrc #2 and cryosparc_P4_J227_map_sharp.mrc #1. Use the ""volume resample"" command to make a copy of one map with the same grid as the other map. volume resample Missing or invalid ""volumes"" argument: empty atom specifier volume morph Missing or invalid ""volumes"" argument: empty atom specifier volume morph #1-10 Map positions are not the same, cryosparc_P4_J272_class_00_00102_volume_sharp (2).mrc #2 and cryosparc_P4_J227_map_sharp.mrc #1. Use the ""volume resample"" command to make a copy of one map with the same grid as the other map. volume #1 level 0.02359 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. GLError( err = 1282, description = b'invalid operation', baseOperation = glDrawBuffer, cArguments = (GL_BACK,) ) Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site- packages/chimerax/core/updateloop.py"", line 73, in draw_new_frame view.draw(check_for_changes = False) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site- packages/chimerax/graphics/view.py"", line 177, in draw self._draw_scene(camera, drawings) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site- packages/chimerax/graphics/view.py"", line 261, in _draw_scene draw_highlight_outline(r, highlight_drawings, color = self._highlight_color, File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site- packages/chimerax/graphics/drawing.py"", line 1609, in draw_highlight_outline r.outline.finish_rendering_outline(color=color, pixel_width=pixel_width) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site- packages/chimerax/graphics/opengl.py"", line 1885, in finish_rendering_outline r.pop_framebuffer() File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site- packages/chimerax/graphics/opengl.py"", line 722, in pop_framebuffer fb.activate() File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site- packages/chimerax/graphics/opengl.py"", line 2271, in activate GL.glDrawBuffer(self._draw_buffer) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1282, description = b'invalid operation', baseOperation = glDrawBuffer, cArguments = (GL_BACK,) ) OpenGL version: 3.3.0 NVIDIA 520.61.05 OpenGL renderer: NVIDIA GeForce RTX 3090/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.9.11 Locale: en_GB.UTF-8 Qt version: PyQt6 6.4.0, Qt 6.4.0 Qt runtime version: 6.4.2 Qt platform: xcb XDG_SESSION_TYPE=x11 DESKTOP_SESSION=ubuntu XDG_SESSION_DESKTOP=ubuntu XDG_CURRENT_DESKTOP=ubuntu:GNOME DISPLAY=:0 Manufacturer: ASUSTeK COMPUTER INC. Model: WS-C621E-SAGE Series OS: Ubuntu 22.04 Jammy Jellyfish Architecture: 64bit ELF Virtual Machine: none CPU: 64 Intel(R) Xeon(R) Silver 4216 CPU @ 2.10GHz Cache Size: 22528 KB Memory: total used free shared buff/cache available Mem: 125Gi 33Gi 69Gi 113Mi 22Gi 90Gi Swap: 15Gi 10Gi 4.6Gi Graphics: 3b:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA102 [GeForce RTX 3090] [10de:2204] (rev a1) Subsystem: eVga.com. Corp. GA102 [GeForce RTX 3090] [3842:3982] Kernel driver in use: nvidia Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 asttokens: 2.2.1 Babel: 2.11.0 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2022.12.7 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.5.8 ChimeraX-AddH: 2.2.3 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.8 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.7 ChimeraX-AtomicLibrary: 10.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 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: 2.7.2 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.1 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.dev202301280224 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3.3 ChimeraX-DockPrep: 1.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 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-ISOLDE: 1.6.dev0 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-LinuxSupport: 1.0.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.0.11 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.11 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.8 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10 ChimeraX-PDB: 2.6.13 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-RenderByAttr: 1.0 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.1 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: 1.10.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.26 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.6 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 comm: 0.1.2 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.6 decorator: 5.1.1 distro: 1.7.0 docutils: 0.19 entrypoints: 0.4 executing: 1.2.0 filelock: 3.7.1 fonttools: 4.38.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.9.26 imagesize: 1.4.1 importlib-metadata: 6.0.0 ipykernel: 6.19.2 ipython: 8.7.0 ipython-genutils: 0.2.0 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 7.4.8 jupyter-core: 5.1.5 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.2 matplotlib: 3.6.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.0 networkx: 2.8.8 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 23.0 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 22.2.2 pkginfo: 1.8.3 platformdirs: 2.6.2 prompt-toolkit: 3.0.36 psutil: 5.9.4 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: 6.4.0 PyQt6-Qt6: 6.4.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.2 python-dateutil: 2.8.2 pytz: 2022.7.1 pyzmq: 25.0.0 qtconsole: 5.4.0 QtPy: 2.3.0 RandomWords: 0.4.0 requests: 2.28.1 scipy: 1.9.3 setuptools: 65.1.1 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 sphinxcontrib-applehelp: 1.0.4 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: 0.6.2 tables: 3.7.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.8.0 urllib3: 1.26.14 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 zipp: 3.12.0" defect closed moderate Graphics can't reproduce all ChimeraX