id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7914 Document Linux compilation system prerequisites such as sqlite to get a working ChimeraX shell tool goddard@… Greg Couch "{{{ The following bug report has been submitted: Platform: Linux-5.4.0-120-generic-x86_64-with-glibc2.31 ChimeraX Version: 1.6.dev202210281747 (2022-10-28 17:47:30 UTC) Description Compiled today's ChimeraX devel source code on Ubuntu 20.04 machine and shell does not work. Fails to import _sqlite3. Log: UCSF ChimeraX version: 1.6.dev202210281747 (2022-10-28) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 1mtx format mmcif fromDatabase pdb 1mtx title: Determination of the three-dimensional structure of margatoxin by 1H, 13C, 15N triple-resonance nuclear magnetic resonance spectroscopy [more info...] Chain information for 1mtx --- Chain | Description | UniProt 1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A 1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A 1.21/A 1.22/A 1.23/A | MARGATOXIN | SCKM_CENMA > close #1.2-30 > show atoms > hide cartoons > ui mousemode right tug Traceback (most recent call last): File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/openmm/openmm.py"", line 14, in swig_import_helper return importlib.import_module(mname) File ""/home/goddard/ucsf/chimerax/ChimeraX.app/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 666, in _load_unlocked File """", line 565, in module_from_spec File """", line 1173, in create_module File """", line 228, in _call_with_frames_removed ImportError: libOpenMM.so.7.7: cannot open shared object file: No such file or directory During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/chimerax/mouse_modes/mousemodes.py"", line 637, in gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_down"") File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/chimerax/mouse_modes/mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/chimerax/tug/tugatoms.py"", line 77, in mouse_down self._pick_atom(pick) File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/chimerax/tug/tugatoms.py"", line 86, in _pick_atom self._tugger = st = StructureTugger(a.structure) File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/chimerax/tug/tugatoms.py"", line 231, in __init__ from openmm import unit File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/openmm/__init__.py"", line 19, in from openmm.openmm import * File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/openmm/openmm.py"", line 17, in _openmm = swig_import_helper() File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/openmm/openmm.py"", line 16, in swig_import_helper return importlib.import_module('_openmm') File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/importlib/__init__.py"", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) ModuleNotFoundError: No module named '_openmm' ModuleNotFoundError: No module named '_openmm' File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/importlib/__init__.py"", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) See log for complete Python traceback. > ui tool show Shell Traceback (most recent call last): File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 560, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/chimerax/core/toolshed/__init__.py"", line 1269, in start_tool return cls._get_func(api, ""start_tool"")(session, ti.name) File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/chimerax/shell/__init__.py"", line 21, in start_tool return ShellUI(session, tool_name) File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/chimerax/shell/tool.py"", line 36, in __init__ from ipykernel.ipkernel import IPythonKernel File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/ipykernel/ipkernel.py"", line 12, in from IPython.core import release File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/IPython/__init__.py"", line 53, in from .terminal.embed import embed File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/IPython/terminal/embed.py"", line 15, in from IPython.core.interactiveshell import DummyMod, InteractiveShell File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/IPython/core/interactiveshell.py"", line 74, in from IPython.core.history import HistoryManager File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/IPython/core/history.py"", line 11, in import sqlite3 File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/sqlite3/__init__.py"", line 57, in from sqlite3.dbapi2 import * File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/sqlite3/dbapi2.py"", line 27, in from _sqlite3 import * ModuleNotFoundError: No module named '_sqlite3' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/chimerax/ui/gui.py"", line 1653, in run(ses, ""ui tool show %s"" % StringArg.unparse(tool_name))) File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/chimerax/ui/cmd.py"", line 219, in ui_tool_show bi.start_tool(session, name) File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 567, in start_tool raise ToolshedError( chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Shell in bundle ChimeraX-Shell: No module named '_sqlite3' chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Shell in bundle ChimeraX-Shell: No module named '_sqlite3' File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 567, in start_tool raise ToolshedError( See log for complete Python traceback. OpenGL version: 4.6 (Core Profile) Mesa 21.2.6 OpenGL renderer: Mesa Intel(R) HD Graphics 6000 (BDW GT3) OpenGL vendor: Intel Python: 3.9.11 Locale: en_US.UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: xcb XDG_SESSION_TYPE=x11 DESKTOP_SESSION=ubuntu XDG_SESSION_DESKTOP=ubuntu XDG_CURRENT_DESKTOP=ubuntu:GNOME DISPLAY=:0 Manufacturer: unknown Model: unknown OS: Ubuntu 20.04 Focal Fossa Architecture: 64bit ELF Virtual Machine: none CPU: 4 Intel(R) Core(TM) i5-5250U CPU @ 1.60GHz Cache Size: 3072 KB Memory: total used free shared buff/cache available Mem: 15Gi 1.2Gi 402Mi 330Mi 13Gi 13Gi Swap: 2.0Gi 2.0Mi 2.0Gi Graphics: 00:02.0 VGA compatible controller [0300]: Intel Corporation HD Graphics 6000 [8086:1626] (rev 09) Subsystem: Intel Corporation HD Graphics 6000 [8086:2057] Kernel driver in use: i915 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 asttokens: 2.0.8 Babel: 2.10.3 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2022.9.24 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.4 ChimeraX-AddH: 2.2.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.3 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.8 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.43.3 ChimeraX-AtomicLibrary: 8.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3 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: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.1 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.dev202210281747 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3 ChimeraX-DockPrep: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 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-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: 1.1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.9 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.8 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.6 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.1 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.1 ChimeraX-PDB: 2.6.8 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: 2.0.1 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 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8 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 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.25.1 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.3 decorator: 5.1.1 distro: 1.7.0 docutils: 0.19 entrypoints: 0.4 executing: 1.1.1 filelock: 3.7.1 fonttools: 4.38.0 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.33 imagecodecs: 2022.7.31 imagesize: 1.4.1 importlib-metadata: 5.0.0 ipykernel: 6.15.3 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 4.11.2 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.5.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.0 networkx: 2.8.5 numexpr: 2.8.4 numpy: 1.23.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.2.0 pip: 22.2.2 pkginfo: 1.8.3 prompt-toolkit: 3.0.31 psutil: 5.9.1 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: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2022.5 pyzmq: 24.0.1 qtconsole: 5.3.1 QtPy: 2.2.1 RandomWords: 0.4.0 requests: 2.28.1 scipy: 1.9.0 setuptools: 65.1.1 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 sphinxcontrib-applehelp: 1.0.2 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: 0.5.1 tables: 3.7.0 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 urllib3: 1.26.12 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 zipp: 3.10.0 }}} " defect assigned normal Build System Zach Pearson all ChimeraX