id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5734 Log and AlphaFold window are blank, plus various deprecation warnings yuliang@… Greg Couch "{{{ The following bug report has been submitted: Platform: Linux-5.15.6-200.fc35.x86_64-x86_64-with-glibc2.34 ChimeraX Version: 1.3rc202111292147 (2021-11-29 21:47:39 UTC) Description The component in log and AlphaFoldRun window could not show up. Log: UCSF ChimeraX version: 1.3rc202111292147 (2021-11-29) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show AlphaFold /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/grako/grammars.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3, and in 3.10 it will stop working from collections import defaultdict, Mapping > alphafold match p51834 /usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/chimerax/core/fetch.py:336: DeprecationWarning: distro.linux_distribution() is deprecated. It should only be used as a compatibility shim with Python's platform.linux_distribution(). Please use distro.id(), distro.version() and distro.name() instead. system = f""{system} {' '.join(distro.linux_distribution())}"" 1 UniProt id does not have an AlphaFold database model: p51834 (UniProt p51834) 1 AlphaFold model found using sequence similarity searches: P9WGF3 (UniProt p51834) Sequence Similarity --- AlphaFold Model| Query Sequence| Identity %| Coverage % SMC_MYCTU | p51834 | 22.1 | 44.4 Opened 1 AlphaFold model /usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/chimerax/geometry/matrix.py:121: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here. Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations from numpy import array, zeros, float > close /usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/chimerax/core/fetch.py:336: DeprecationWarning: distro.linux_distribution() is deprecated. It should only be used as a compatibility shim with Python's platform.linux_distribution(). Please use distro.id(), distro.version() and distro.name() instead. system = f""{system} {' '.join(distro.linux_distribution())}"" Fetching p51834 UniProt info from https://www.uniprot.org/uniprot/p51834.xml > alphafold predict p51834 /usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/chimerax/bug_reporter/bug_reporter_gui.py:718: ResourceWarning: unclosed file <_io.TextIOWrapper name='/sys/devices/virtual/dmi/id/sys_vendor' mode='r' encoding='utf-8'> vendor = open(dmi_prefix + ""sys_vendor"", encoding='utf-8').read().strip() ResourceWarning: Enable tracemalloc to get the object allocation traceback /usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/chimerax/bug_reporter/bug_reporter_gui.py:723: ResourceWarning: unclosed file <_io.TextIOWrapper name='/sys/devices/virtual/dmi/id/product_name' mode='r' encoding='utf-8'> product = open(dmi_prefix + ""product_name"", encoding='utf-8').read().strip() ResourceWarning: Enable tracemalloc to get the object allocation traceback /usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/chimerax/bug_reporter/bug_reporter_gui.py:730: DeprecationWarning: distro.linux_distribution() is deprecated. It should only be used as a compatibility shim with Python's platform.linux_distribution(). Please use distro.id(), distro.version() and distro.name() instead. OS: {' '.join(distro.linux_distribution())} > alphafold predict p51834 /usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/chimerax/core/fetch.py:336: DeprecationWarning: distro.linux_distribution() is deprecated. It should only be used as a compatibility shim with Python's platform.linux_distribution(). Please use distro.id(), distro.version() and distro.name() instead. system = f""{system} {' '.join(distro.linux_distribution())}"" > open /home/yl2/Downloads/5xg3.pdb 5xg3.pdb title: Crystal structure of the atpgs-engaged SMC head domain with an extended coiled coil bound to the C-terminal domain of SCPA derived from bacillus subtilis [more info...] | Chain information for 5xg3.pdb #1 --- Chain | Description | UniProt A | chromosome partition protein SMC | SMC_BACSU B | chromosome partition protein SMC | SMC_BACSU C | segregation and condensation protein A | D | segregation and condensation protein A | Non-standard residues in 5xg3.pdb #1 --- AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine 5'-(3-thiotriphosphate);adenosine 5'-(γ-thiotriphosphate); adenosine-5'-diphosphate monothiophosphate) CO — cobalt (II) ion MG — magnesium ion /usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/chimerax/geometry/matrix.py:121: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here. Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations from numpy import array, zeros, float /usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/chimerax/bug_reporter/bug_reporter_gui.py:718: ResourceWarning: unclosed file <_io.TextIOWrapper name='/sys/devices/virtual/dmi/id/sys_vendor' mode='r' encoding='utf-8'> vendor = open(dmi_prefix + ""sys_vendor"", encoding='utf-8').read().strip() ResourceWarning: Enable tracemalloc to get the object allocation traceback /usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/chimerax/bug_reporter/bug_reporter_gui.py:723: ResourceWarning: unclosed file <_io.TextIOWrapper name='/sys/devices/virtual/dmi/id/product_name' mode='r' encoding='utf-8'> product = open(dmi_prefix + ""product_name"", encoding='utf-8').read().strip() ResourceWarning: Enable tracemalloc to get the object allocation traceback /usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/chimerax/bug_reporter/bug_reporter_gui.py:730: DeprecationWarning: distro.linux_distribution() is deprecated. It should only be used as a compatibility shim with Python's platform.linux_distribution(). Please use distro.id(), distro.version() and distro.name() instead. OS: {' '.join(distro.linux_distribution())} OpenGL version: 4.6 (Core Profile) Mesa 21.2.5 OpenGL renderer: Mesa Intel(R) HD Graphics 5500 (BDW GT2) OpenGL vendor: Intel Manufacturer: LENOVO Model: 20BSCTO1WW OS: Fedora Linux 35 Architecture: 64bit ELF Virutal Machine: none CPU: 4 Intel(R) Core(TM) i5-5300U CPU @ 2.30GHz Cache Size: 3072 KB Memory: total used free shared buff/cache available Mem: 7.6Gi 2.7Gi 1.0Gi 1.5Gi 3.9Gi 3.2Gi Swap: 14Gi 0B 14Gi Graphics: 00:02.0 VGA compatible controller [0300]: Intel Corporation HD Graphics 5500 [8086:1616] (rev 09) Subsystem: Lenovo Device [17aa:2227] 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: 2021.10.8 cftime: 1.5.1.1 charset-normalizer: 2.0.8 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.3 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.31 ChimeraX-AtomicLibrary: 4.2 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3rc202111292147 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 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: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 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 ChimeraX-Label: 1.1 ChimeraX-LinuxSupport: 1.0 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 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: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 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 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.6.1 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: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.2.1 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 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: 0.4.4 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 distro: 1.6.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 line-profiler: 3.3.0 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.7.3 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.3 ParmEd: 3.2.0 parso: 0.8.2 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 psutil: 5.8.0 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.2 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 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: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 File attachment: Screenshot from 2021-12-06 00-03-55.png }}} [attachment:""Screenshot from 2021-12-06 00-03-55.png""] " defect closed normal Core limitation chimera-programmers all ChimeraX