id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4383 "Toolshed error in ""already installed"" error message" long.han@… Greg Couch "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-1127.13.1.el7.x86_64-x86_64-with-glibc2.14 ChimeraX Version: 1.2.dev202102200332 (2021-02-20 03:32:07 UTC) Description The Stringdb cannot be installed on this workstation. Thanks Log: UCSF ChimeraX version: 1.2.dev202102200332 (2021-02-20) © 2016-2020 Regents of the University of California. All rights reserved. > open for-inter.cxs Log from Thu Mar 18 12:28:19 2021UCSF ChimeraX version: 1.2.dev202102200332 (2021-02-20) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > toolshed show Downloading bundle ChimeraX_Cytoscape-0.1-py3-none-any.whl Successfully installed ChimeraX-Cytoscape-0.1 Installed ChimeraX-Cytoscape (0.1) Downloading bundle ChimeraX_Stringdb-0.1-py3-none-any.whl Successfully installed ChimeraX-Stringdb-0.1 Installed ChimeraX-Stringdb (0.1) > open C1_omp.cif Summary of feedback from opening C1_omp.cif --- warnings | Unknown polymer entity '1' near line 506 Unknown polymer entity '2' near line 123269 Unknown polymer entity '3' near line 135295 Unknown polymer entity '4' near line 141013 Unknown polymer entity '5' near line 145207 64 messages similar to the above omitted Atom . is not in the residue template for LYS /0T:501 Atom . is not in the residue template for LYS /0U:501 Atom . is not in the residue template for LYS /0V:501 Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. Chain information for C1_omp.cif #1 --- Chain | Description 0A 0B 0C 0D 0E 0F 0G 0H 0I 0J 0K 0L 0M 0N 0O 0P 0Q 0R 0S 0T 0U 0V 0W 0X 0Y 0Z 1A 1B 1C 1D 1E 1F 1G | ? 1H 1I 6D | ? 1J 1K | ? 1L 1M | ? 1N | ? 1O | ? 1P | ? 1Q | ? 1R | ? 1S | ? 1T | ? 1U | ? 1V 5W 5X 5Y | ? 1W | ? 1X | ? 1Y | ? 1Z | ? 2A | ? 2B | ? 2C | ? 2D | ? 2E | ? 2P | ? 2Q 2R | ? 2S 2U | ? 2T 2V | ? 2W 2X | ? 2Y 2Z | ? 3A 3B | ? 3C 3D | ? 3E | ? 3F | ? 3G | ? 3H | ? 3I | ? 3J 3K | ? 3L | ? 3M 3N | ? 3O | ? 3P 3Q | ? 3R | ? 3S 3T | ? 3U | ? 3V 3W | ? 3X 3Y 3Z | ? 4A 4B | ? 4C | ? 4D | ? 4E | ? 4F 4G 4H | ? 4I 4J 4K 4L 4M 4N | ? 4O | ? 4P | ? 4Q 4R 4S | ? 4T 4U 4V | ? 4W 4X 4Y 4Z | ? 5A 5B 5C 5D | ? 5E 5F 5G 5H | ? 5I 5J 5K 5L | ? 5M 5N 5O | ? 5P 5Q 5R 5S 5T 5U | ? 5V | ? 5Z | ? 6A 6B | ? 6C | ? 6E 6F | ? 6G 6H 6I 6J | ? 6K 6L | ? 6M 6N | ? > rename #1 id #2 > color #2/3M-3Z,4A-4B #2f6eaf > color #2/4E-4H #c0ece6 > color #2/4I-4P #762670 > color #2/4Q-4S #006f69 > color #2/4T-4V #ea8185 > color #2/4W-4Z,5A-5D #e75f0f > color #2/5E-5H #8bbb26 > color #2/5I-5L #f1e81d > color #2/ 5M-5U,5V #f554f4 > color #2/4D #f1912d > color #2/4C 9a458f Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color #2/5W-5Y #65c1c5 > color #2/5Z #202876 > color #2/0A-0Z,1A-1G #f0027f > color #2/1H-1I,6D #23eced > color #2/1P #14f403 > color #2/1O #dc6e07 > color #2/1N #a651a8 > color #2/1Q #5e61c1 > color #2/1T-1Z,2A-2E #a2512d > color #2/1J-1K #8bbb26 > color #2/1L-1M #1596d3 > color #2/6A-6C #861a7f > color #2/6E-6F #eced55 > color #2/6M-6N #18489a > color #2/6K-6L #e15541 > color #2/6G-6J #1b9c91 > color #2/2S-2V #868bd3 > color #2/3C-3D #c5a322 > color #2/3E #3c99dd > color #2/3F-3G #efea3b > color #2/3L #d5161c > color #2/3J-3K #247235 > color #2/3H,3I #eb1c1a > color #2/1R-1S #f18209 > hide #1 atoms > show #1 cartoons > hide #2 atoms > show #2 cartoons > set bgColor white > material dull > lighting gentle intensity 0.6 ambientIntensity 0.8 fillIntensity 0.3 > graphics silhouettes false > preset cylinders Changed 468515 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > cartoon style coil xsection oval thickness 2 > cartoon style strand xsection rectangle width 3 > cartoon style strand xsection rectangle thickness 2 > size pseudobondRadius 0.65 Changed 440 pseudobond radii > lighting soft ambientIntensity 0.8 intensity 1.0 multiShadow 512 > save for-inter.cxs ——— End of log from Thu Mar 18 12:28:19 2021 ——— opened ChimeraX session > toolshed show Downloading bundle ChimeraX_Stringdb-0.1-py3-none-any.whl Traceback (most recent call last): File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/chimerax/help_viewer/tool.py"", line 369, in item.finished.connect(lambda *args, **kw: self.download_finished(*args, **kw, item=item, is_wheel=is_wheel)) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/chimerax/help_viewer/tool.py"", line 410, in download_finished self.session.toolshed.install_bundle(filename, File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/chimerax/core/toolshed/__init__.py"", line 898, in install_bundle _install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall, session=session, no_deps=no_deps) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/chimerax/toolshed_utils/__init__.py"", line 219, in _install_bundle raise ToolshedInstalledError(""bundle %r already installed"" % bundle_name) chimerax.core.toolshed.ToolshedInstalledError: bundle '/home/spuser/Downloads/ChimeraX_Stringdb-0.1-py3-none-any.whl' already installed chimerax.core.toolshed.ToolshedInstalledError: bundle '/home/spuser/Downloads/ChimeraX_Stringdb-0.1-py3-none-any.whl' already installed File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/chimerax/toolshed_utils/__init__.py"", line 219, in _install_bundle raise ToolshedInstalledError(""bundle %r already installed"" % bundle_name) See log for complete Python traceback. Downloading bundle ChimeraX_Stringdb-0.1-py3-none-any.whl Traceback (most recent call last): File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/chimerax/help_viewer/tool.py"", line 369, in item.finished.connect(lambda *args, **kw: self.download_finished(*args, **kw, item=item, is_wheel=is_wheel)) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/chimerax/help_viewer/tool.py"", line 410, in download_finished self.session.toolshed.install_bundle(filename, File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/chimerax/core/toolshed/__init__.py"", line 898, in install_bundle _install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall, session=session, no_deps=no_deps) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/chimerax/toolshed_utils/__init__.py"", line 219, in _install_bundle raise ToolshedInstalledError(""bundle %r already installed"" % bundle_name) chimerax.core.toolshed.ToolshedInstalledError: bundle '/home/spuser/Downloads/ChimeraX_Stringdb-0.1-py3-none-any.whl' already installed chimerax.core.toolshed.ToolshedInstalledError: bundle '/home/spuser/Downloads/ChimeraX_Stringdb-0.1-py3-none-any.whl' already installed File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/chimerax/toolshed_utils/__init__.py"", line 219, in _install_bundle raise ToolshedInstalledError(""bundle %r already installed"" % bundle_name) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 460.32.03 OpenGL renderer: GeForce GTX 1080 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Supermicro Model: SYS-7048GR-TR OS: CentOS Linux 7 Core Architecture: 64bit ELF Virutal Machine: none CPU: 48 Intel(R) Xeon(R) CPU E5-2650 v4 @ 2.20GHz Cache Size: 30720 KB Memory: total used free shared buff/cache available Mem: 377G 145G 94G 386M 137G 230G Swap: 19G 486M 19G Graphics: 02:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [GeForce GTX 1080 Ti] [10de:1b06] (rev a1) Subsystem: ASUSTeK Computer Inc. Device [1043:85e5] Kernel driver in use: nvidia Locale: ('en_US', 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.9.0 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.12.5 cftime: 1.4.1 chardet: 3.0.4 ChimeraX-AddCharge: 1.0 ChimeraX-AddH: 2.1.4 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: 1.11.1 ChimeraX-AtomicLibrary: 2.0 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 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-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.0 ChimeraX-CommandLine: 1.1.3 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2.dev202102200332 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.0.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-Cytoscape: 0.1 ChimeraX-DataFormats: 1.1 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: 2.1 ChimeraX-Help: 1.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0 ChimeraX-Label: 1.0 ChimeraX-LinuxSupport: 1.0 ChimeraX-ListInfo: 1.1 ChimeraX-Log: 1.1.1 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: 1.1 ChimeraX-MDcrds: 2.2 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: 1.0.1 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: 1.5 ChimeraX-PDB: 2.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 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 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Stringdb: 0.1 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 ChimeraX-ToolshedUtils: 1.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.6.1 ChimeraX-uniprot: 2.1 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: 4.4.2 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: 1.1.1 matplotlib: 3.3.2 msgpack: 1.0.0 netCDF4: 1.5.4 networkx: 2.5 numexpr: 2.7.2 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: 3.0.16 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 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: 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: 2020.9.3 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 Tool Shed duplicate Eric Pettersen Scooter Morris all ChimeraX