Changes between Initial Version and Version 2 of Ticket #15329


Ignore:
Timestamp:
May 30, 2024, 2:33:33 PM (17 months ago)
Author:
Greg Couch
Comment:

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  • Ticket #15329

    • Property Component Unassigned → Platform
    • Property Owner set to Greg Couch
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → accepted
    • Property Summary ChimeraX bug report submission → Flatpak suggestions
    • Property Type defect → enhancement

  • Ticket #15329 – Description

    initial v2  
    1 {{{
    2 The following bug report has been submitted:
    3 Platform:        Linux-6.8.0-31-generic-x86_64-with-glibc2.38
    4 ChimeraX Version: 1.8rc202405250712 (2024-05-25 07:12:25 UTC)
    5 Description
    61Not really a bug, but more of a GUI issue/suggestion, the app icon doesn't appear when you install the flatpack version, nor it "respects" dark mode on Ubuntu
    72
    8 Log:
    9 Startup Messages 
    10 --- 
    11 note | available bundle cache has not been initialized yet 
    12  
    13 UCSF ChimeraX version: 1.8rc202405250712 (2024-05-25) 
    14 © 2016-2024 Regents of the University of California. All rights reserved. 
    15 How to cite UCSF ChimeraX 
    16 
    17 > open /home/azinas/Downloads/J141_ready.mrc
    18 
    19 Opened J141_ready.mrc as #1, grid size 331,331,331, pixel 1, shown at level
    20 1.87, step 2, values float32 
    21 
    22 > open /home/azinas/Downloads/J92/post_ready.mrc format mrc
    23 
    24 Opened post_ready.mrc as #2, grid size 331,331,331, pixel 1, shown at level
    25 2.39, step 2, values float32 
    26 
    27 > volume #2 color #99c1f1
    28 
    29 > lighting soft
    30 
    31 > volume #1 step 1
    32 
    33 > volume #2 step 1
    34 
    35 > volume #1 level 4.086
    36 
    37 > open /home/azinas/Downloads/dwbready-fitted.pdb format pdb
    38 
    39 Chain information for dwbready-fitted.pdb #3 
    40 --- 
    41 Chain | Description 
    42 A B C D E F | No description available 
    43 Aa | No description available 
    44 Ap | No description available 
    45 Aq | No description available 
    46 Ba Bb Bd Bi | No description available 
    47 Bc | No description available 
    48 Be | No description available 
    49 Bf | No description available 
    50 Bg Bk | No description available 
    51 Bh | No description available 
    52 Bj | No description available 
    53 Bl | No description available 
    54 Bm | No description available 
    55 Bn | No description available 
    56 a | No description available 
    57 b | No description available 
    58 c | No description available 
    59 d | No description available 
    60 e | No description available 
    61 f | No description available 
    62  
    63 
    64 > show cartoons
    65 
    66 > hide atoms
    67 
    68 
    69 
    70 
     3{{{
    714OpenGL version: 3.3.0 NVIDIA 535.171.04
    725OpenGL renderer: NVIDIA GeForce RTX 4090/PCIe/SSE2
    … …  
    10033        Subsystem: NVIDIA Corporation Device [10de:16f3]       
    10134        Kernel driver in use: nvidia
    102 
    103 Installed Packages:
    104     alabaster: 0.7.16
    105     appdirs: 1.4.4
    106     asttokens: 2.4.1
    107     Babel: 2.15.0
    108     beautifulsoup4: 4.12.3
    109     blockdiag: 3.0.0
    110     blosc2: 2.0.0
    111     build: 1.2.1
    112     certifi: 2024.2.2
    113     cftime: 1.6.3
    114     charset-normalizer: 3.3.2
    115     ChimeraX-AddCharge: 1.5.17
    116     ChimeraX-AddH: 2.2.6
    117     ChimeraX-AlignmentAlgorithms: 2.0.2
    118     ChimeraX-AlignmentHdrs: 3.5
    119     ChimeraX-AlignmentMatrices: 2.1
    120     ChimeraX-Alignments: 2.12.7
    121     ChimeraX-AlphaFold: 1.0
    122     ChimeraX-AltlocExplorer: 1.1.1
    123     ChimeraX-AmberInfo: 1.0
    124     ChimeraX-Arrays: 1.1
    125     ChimeraX-Atomic: 1.57
    126     ChimeraX-AtomicLibrary: 14.0.5
    127     ChimeraX-AtomSearch: 2.0.1
    128     ChimeraX-AxesPlanes: 2.4
    129     ChimeraX-BasicActions: 1.1.2
    130     ChimeraX-BILD: 1.0
    131     ChimeraX-BlastProtein: 2.4.6
    132     ChimeraX-BondRot: 2.0.4
    133     ChimeraX-BugReporter: 1.0.1
    134     ChimeraX-BuildStructure: 2.12.1
    135     ChimeraX-Bumps: 1.0
    136     ChimeraX-BundleBuilder: 1.2.7
    137     ChimeraX-ButtonPanel: 1.0.1
    138     ChimeraX-CageBuilder: 1.0.1
    139     ChimeraX-CellPack: 1.0
    140     ChimeraX-Centroids: 1.4
    141     ChimeraX-ChangeChains: 1.1
    142     ChimeraX-CheckWaters: 1.4
    143     ChimeraX-ChemGroup: 2.0.1
    144     ChimeraX-Clashes: 2.2.4
    145     ChimeraX-Clipper: 0.23.0
    146     ChimeraX-ColorActions: 1.0.5
    147     ChimeraX-ColorGlobe: 1.0
    148     ChimeraX-ColorKey: 1.5.6
    149     ChimeraX-CommandLine: 1.2.5
    150     ChimeraX-ConnectStructure: 2.0.1
    151     ChimeraX-Contacts: 1.0.1
    152     ChimeraX-Core: 1.8rc202405250712
    153     ChimeraX-CoreFormats: 1.2
    154     ChimeraX-coulombic: 1.4.3
    155     ChimeraX-Crosslinks: 1.0
    156     ChimeraX-Crystal: 1.0
    157     ChimeraX-CrystalContacts: 1.0.1
    158     ChimeraX-DataFormats: 1.2.3
    159     ChimeraX-Dicom: 1.2.4
    160     ChimeraX-DiffPlot: 1.0
    161     ChimeraX-DistMonitor: 1.4.2
    162     ChimeraX-DockPrep: 1.1.3
    163     ChimeraX-Dssp: 2.0
    164     ChimeraX-EMDB-SFF: 1.0
    165     ChimeraX-ESMFold: 1.0
    166     ChimeraX-FileHistory: 1.0.1
    167     ChimeraX-FunctionKey: 1.0.1
    168     ChimeraX-Geometry: 1.3
    169     ChimeraX-gltf: 1.0
    170     ChimeraX-Graphics: 1.1.1
    171     ChimeraX-Hbonds: 2.4
    172     ChimeraX-Help: 1.2.2
    173     ChimeraX-HKCage: 1.3
    174     ChimeraX-IHM: 1.1
    175     ChimeraX-ImageFormats: 1.2
    176     ChimeraX-IMOD: 1.0
    177     ChimeraX-IO: 1.0.1
    178     ChimeraX-ISOLDE: 1.8.dev0
    179     ChimeraX-ItemsInspection: 1.0.1
    180     ChimeraX-IUPAC: 1.0
    181     ChimeraX-Label: 1.1.10
    182     ChimeraX-LinuxSupport: 1.0.1
    183     ChimeraX-ListInfo: 1.2.2
    184     ChimeraX-Log: 1.1.6
    185     ChimeraX-LookingGlass: 1.1
    186     ChimeraX-Maestro: 1.9.1
    187     ChimeraX-Map: 1.2
    188     ChimeraX-MapData: 2.0
    189     ChimeraX-MapEraser: 1.0.1
    190     ChimeraX-MapFilter: 2.0.1
    191     ChimeraX-MapFit: 2.0
    192     ChimeraX-MapSeries: 2.1.1
    193     ChimeraX-Markers: 1.0.1
    194     ChimeraX-Mask: 1.0.2
    195     ChimeraX-MatchMaker: 2.1.3
    196     ChimeraX-MCopy: 1.0
    197     ChimeraX-MDcrds: 2.7.1
    198     ChimeraX-MedicalToolbar: 1.0.2
    199     ChimeraX-Meeting: 1.0.1
    200     ChimeraX-MLP: 1.1.1
    201     ChimeraX-mmCIF: 2.14.1
    202     ChimeraX-MMTF: 2.2
    203     ChimeraX-Modeller: 1.5.16
    204     ChimeraX-ModelPanel: 1.5
    205     ChimeraX-ModelSeries: 1.0.1
    206     ChimeraX-Mol2: 2.0.3
    207     ChimeraX-Mole: 1.0
    208     ChimeraX-Morph: 1.0.2
    209     ChimeraX-MouseModes: 1.2
    210     ChimeraX-Movie: 1.0
    211     ChimeraX-Neuron: 1.0
    212     ChimeraX-Nifti: 1.2
    213     ChimeraX-NMRSTAR: 1.0.2
    214     ChimeraX-NRRD: 1.2
    215     ChimeraX-Nucleotides: 2.0.3
    216     ChimeraX-OpenCommand: 1.13.4
    217     ChimeraX-PDB: 2.7.5
    218     ChimeraX-PDBBio: 1.0.1
    219     ChimeraX-PDBLibrary: 1.0.4
    220     ChimeraX-PDBMatrices: 1.0
    221     ChimeraX-PickBlobs: 1.0.1
    222     ChimeraX-Positions: 1.0
    223     ChimeraX-PresetMgr: 1.1.1
    224     ChimeraX-PubChem: 2.2
    225     ChimeraX-ReadPbonds: 1.0.1
    226     ChimeraX-Registration: 1.1.2
    227     ChimeraX-RemoteControl: 1.0
    228     ChimeraX-RenderByAttr: 1.4.1
    229     ChimeraX-RenumberResidues: 1.1
    230     ChimeraX-ResidueFit: 1.0.1
    231     ChimeraX-RestServer: 1.2
    232     ChimeraX-RNALayout: 1.0
    233     ChimeraX-RotamerLibMgr: 4.0
    234     ChimeraX-RotamerLibsDunbrack: 2.0
    235     ChimeraX-RotamerLibsDynameomics: 2.0
    236     ChimeraX-RotamerLibsRichardson: 2.0
    237     ChimeraX-SaveCommand: 1.5.1
    238     ChimeraX-SchemeMgr: 1.0
    239     ChimeraX-SDF: 2.0.2
    240     ChimeraX-Segger: 1.0
    241     ChimeraX-Segment: 1.0.1
    242     ChimeraX-Segmentations: 3.0.12
    243     ChimeraX-SelInspector: 1.0
    244     ChimeraX-SeqView: 2.11.2
    245     ChimeraX-Shape: 1.0.1
    246     ChimeraX-Shell: 1.0.1
    247     ChimeraX-Shortcuts: 1.1.1
    248     ChimeraX-ShowSequences: 1.0.3
    249     ChimeraX-SideView: 1.0.1
    250     ChimeraX-Smiles: 2.1.2
    251     ChimeraX-SmoothLines: 1.0
    252     ChimeraX-SpaceNavigator: 1.0
    253     ChimeraX-StdCommands: 1.16.5
    254     ChimeraX-STL: 1.0.1
    255     ChimeraX-Storm: 1.0
    256     ChimeraX-StructMeasure: 1.2.1
    257     ChimeraX-Struts: 1.0.1
    258     ChimeraX-Surface: 1.0.1
    259     ChimeraX-SwapAA: 2.0.1
    260     ChimeraX-SwapRes: 2.5
    261     ChimeraX-TapeMeasure: 1.0
    262     ChimeraX-TaskManager: 1.0
    263     ChimeraX-Test: 1.0
    264     ChimeraX-Toolbar: 1.1.2
    265     ChimeraX-ToolshedUtils: 1.2.4
    266     ChimeraX-Topography: 1.0
    267     ChimeraX-ToQuest: 1.0
    268     ChimeraX-Tug: 1.0.1
    269     ChimeraX-UI: 1.39.1
    270     ChimeraX-uniprot: 2.3
    271     ChimeraX-UnitCell: 1.0.1
    272     ChimeraX-ViewDockX: 1.4.2
    273     ChimeraX-VIPERdb: 1.0
    274     ChimeraX-Vive: 1.1
    275     ChimeraX-VolumeMenu: 1.0.1
    276     ChimeraX-vrml: 1.0
    277     ChimeraX-VTK: 1.0
    278     ChimeraX-WavefrontOBJ: 1.0
    279     ChimeraX-WebCam: 1.0.2
    280     ChimeraX-WebServices: 1.1.4
    281     ChimeraX-Zone: 1.0.1
    282     colorama: 0.4.6
    283     comm: 0.2.2
    284     contourpy: 1.2.1
    285     cxservices: 1.2.2
    286     cycler: 0.12.1
    287     Cython: 3.0.10
    288     debugpy: 1.8.1
    289     decorator: 5.1.1
    290     distro: 1.9.0
    291     docutils: 0.20.1
    292     executing: 2.0.1
    293     filelock: 3.13.4
    294     fonttools: 4.52.4
    295     funcparserlib: 2.0.0a0
    296     glfw: 2.7.0
    297     grako: 3.16.5
    298     h5py: 3.11.0
    299     html2text: 2024.2.26
    300     idna: 3.7
    301     ihm: 1.0
    302     imagecodecs: 2024.1.1
    303     imagesize: 1.4.1
    304     ipykernel: 6.29.2
    305     ipython: 8.21.0
    306     ipywidgets: 8.1.3
    307     jedi: 0.19.1
    308     jinja2: 3.1.4
    309     jupyter-client: 8.6.0
    310     jupyter-core: 5.7.2
    311     jupyterlab-widgets: 3.0.11
    312     kiwisolver: 1.4.5
    313     line-profiler: 4.1.2
    314     lxml: 5.2.1
    315     lz4: 4.3.3
    316     MarkupSafe: 2.1.5
    317     matplotlib: 3.8.4
    318     matplotlib-inline: 0.1.7
    319     msgpack: 1.0.8
    320     nest-asyncio: 1.6.0
    321     netCDF4: 1.6.5
    322     networkx: 3.3
    323     nibabel: 5.2.0
    324     nptyping: 2.5.0
    325     numexpr: 2.10.0
    326     numpy: 1.26.4
    327     openvr: 1.26.701
    328     packaging: 24.0
    329     ParmEd: 4.2.2
    330     parso: 0.8.4
    331     pep517: 0.13.1
    332     pexpect: 4.9.0
    333     pillow: 10.3.0
    334     pip: 24.0
    335     pkginfo: 1.10.0
    336     platformdirs: 4.2.2
    337     prompt-toolkit: 3.0.44
    338     psutil: 5.9.8
    339     ptyprocess: 0.7.0
    340     pure-eval: 0.2.2
    341     py-cpuinfo: 9.0.0
    342     pycollada: 0.8
    343     pydicom: 2.4.4
    344     pygments: 2.17.2
    345     pynmrstar: 3.3.4
    346     pynrrd: 1.0.0
    347     PyOpenGL: 3.1.7
    348     PyOpenGL-accelerate: 3.1.7
    349     pyopenxr: 1.0.3401
    350     pyparsing: 3.1.2
    351     pyproject-hooks: 1.1.0
    352     PyQt6: 6.6.1
    353     PyQt6-Qt6: 6.6.3
    354     PyQt6-sip: 13.6.0
    355     PyQt6-WebEngine: 6.6.0
    356     PyQt6-WebEngine-Qt6: 6.6.3
    357     python-dateutil: 2.9.0.post0
    358     pytz: 2024.1
    359     pyzmq: 26.0.3
    360     qtconsole: 5.5.1
    361     QtPy: 2.4.1
    362     RandomWords: 0.4.0
    363     requests: 2.31.0
    364     scipy: 1.13.0
    365     setuptools: 69.5.1
    366     sfftk-rw: 0.8.1
    367     six: 1.16.0
    368     snowballstemmer: 2.2.0
    369     sortedcontainers: 2.4.0
    370     soupsieve: 2.5
    371     sphinx: 7.2.6
    372     sphinx-autodoc-typehints: 2.0.1
    373     sphinxcontrib-applehelp: 1.0.8
    374     sphinxcontrib-blockdiag: 3.0.0
    375     sphinxcontrib-devhelp: 1.0.6
    376     sphinxcontrib-htmlhelp: 2.0.5
    377     sphinxcontrib-jsmath: 1.0.1
    378     sphinxcontrib-qthelp: 1.0.7
    379     sphinxcontrib-serializinghtml: 1.1.10
    380     stack-data: 0.6.3
    381     superqt: 0.6.3
    382     tables: 3.8.0
    383     tcia-utils: 1.5.1
    384     tifffile: 2024.1.30
    385     tinyarray: 1.2.4
    386     tornado: 6.4
    387     traitlets: 5.14.2
    388     typing-extensions: 4.12.0
    389     tzdata: 2024.1
    390     urllib3: 2.2.1
    391     wcwidth: 0.2.13
    392     webcolors: 1.13
    393     wheel: 0.43.0
    394     wheel-filename: 1.4.1
    395     widgetsnbextension: 4.0.11
    39635}}}