Changes between Initial Version and Version 1 of Ticket #10096


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Timestamp:
Nov 6, 2023, 12:41:43 PM (2 years ago)
Author:
Tom Goddard
Comment:

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  • Ticket #10096

    • Property Cc Elaine Meng added
    • Property Component Unassigned → Volume Data
    • Property Owner set to Tom Goddard
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Reporter changed from goddard@… to jhooker@…
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → Allow setting initial volume colors
    • Property Type defect → enhancement

  • Ticket #10096 – Description

    initial v1  
    1 {{{
    2 The following bug report has been submitted:
    3 Platform:        macOS-13.5.2-x86_64-i386-64bit
    4 ChimeraX Version: 1.7.dev202310231853 (2023-10-23 18:53:46 UTC)
    5 Description
    6 Allow setting the initial colors when volumes are opened using the volume command.
     1From: James Hooker via ChimeraX-users <chimerax-users@cgl.ucsf.edu>
     2Subject: [chimerax-users] Change default colour cycle for EM maps
     3Date: November 6, 2023 at 4:38:13 AM PST
     4To: chimerax-users@cgl.ucsf.edu
     5Reply-To: James Hooker
    76
    8 Log:
    9 Could not find tool "Tabbed Toolbar" 
    10 UCSF ChimeraX version: 1.7.dev202310231853 (2023-10-23) 
    11 © 2016-2023 Regents of the University of California. All rights reserved. 
    12 How to cite UCSF ChimeraX 
     7Hello all,
    138
    14 > volume initialColors salmon,lime,#ffff00
     9I am looking for a way to change the qualitative colour cycle in ChimeraX from the default (grey, yellow, blue, purple, pink, …).
     10I have flicked through the online documentation, but have not yet found a solution.
     11Many people must have desired to do this at some point, right?
     12Any advice is welcome!
    1513
    16 
    17 
    18 
    19 OpenGL version: 4.1 ATI-4.14.1
    20 OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
    21 OpenGL vendor: ATI Technologies Inc.
    22 
    23 Python: 3.11.2
    24 Locale: en_US.UTF-8
    25 Qt version: PyQt6 6.3.1, Qt 6.3.1
    26 Qt runtime version: 6.3.2
    27 Qt platform: cocoa
    28 Hardware:
    29 
    30     Hardware Overview:
    31 
    32       Model Name: iMac
    33       Model Identifier: iMac18,3
    34       Processor Name: Quad-Core Intel Core i7
    35       Processor Speed: 4.2 GHz
    36       Number of Processors: 1
    37       Total Number of Cores: 4
    38       L2 Cache (per Core): 256 KB
    39       L3 Cache: 8 MB
    40       Hyper-Threading Technology: Enabled
    41       Memory: 32 GB
    42       System Firmware Version: 515.0.0.0.0
    43       OS Loader Version: 577.140.2~15
    44       SMC Version (system): 2.41f2
    45 
    46 Software:
    47 
    48     System Software Overview:
    49 
    50       System Version: macOS 13.5.2 (22G91)
    51       Kernel Version: Darwin 22.6.0
    52       Time since boot: 59 days, 18 hours, 4 minutes
    53 
    54 Graphics/Displays:
    55 
    56     Radeon Pro 580:
    57 
    58       Chipset Model: Radeon Pro 580
    59       Type: GPU
    60       Bus: PCIe
    61       PCIe Lane Width: x16
    62       VRAM (Total): 8 GB
    63       Vendor: AMD (0x1002)
    64       Device ID: 0x67df
    65       Revision ID: 0x00c0
    66       ROM Revision: 113-D000AA-931
    67       VBIOS Version: 113-D0001A1X-025
    68       EFI Driver Version: 01.00.931
    69       Metal Support: Metal 2
    70       Displays:
    71         iMac:
    72           Display Type: Built-In Retina LCD
    73           Resolution: Retina 5K (5120 x 2880)
    74           Framebuffer Depth: 30-Bit Color (ARGB2101010)
    75           Main Display: Yes
    76           Mirror: Off
    77           Online: Yes
    78           Automatically Adjust Brightness: Yes
    79           Connection Type: Internal
    80 
    81 
    82 Installed Packages:
    83     alabaster: 0.7.13
    84     appdirs: 1.4.4
    85     appnope: 0.1.3
    86     asttokens: 2.4.0
    87     Babel: 2.13.0
    88     backcall: 0.2.0
    89     beautifulsoup4: 4.11.2
    90     blockdiag: 3.0.0
    91     blosc2: 2.0.0
    92     build: 0.10.0
    93     certifi: 2022.12.7
    94     cftime: 1.6.3
    95     charset-normalizer: 3.3.1
    96     ChimeraX-AddCharge: 1.5.12
    97     ChimeraX-AddH: 2.2.5
    98     ChimeraX-AlignmentAlgorithms: 2.0.1
    99     ChimeraX-AlignmentHdrs: 3.4.1
    100     ChimeraX-AlignmentMatrices: 2.1
    101     ChimeraX-Alignments: 2.12.1
    102     ChimeraX-AlphaFold: 1.0
    103     ChimeraX-AltlocExplorer: 1.1.1
    104     ChimeraX-AmberInfo: 1.0
    105     ChimeraX-Arrays: 1.1
    106     ChimeraX-Atomic: 1.49
    107     ChimeraX-AtomicLibrary: 11.0
    108     ChimeraX-AtomSearch: 2.0.1
    109     ChimeraX-AxesPlanes: 2.3.2
    110     ChimeraX-BasicActions: 1.1.2
    111     ChimeraX-BILD: 1.0
    112     ChimeraX-BlastProtein: 2.1.2
    113     ChimeraX-BondRot: 2.0.4
    114     ChimeraX-BugReporter: 1.0.1
    115     ChimeraX-BuildStructure: 2.10.5
    116     ChimeraX-Bumps: 1.0
    117     ChimeraX-BundleBuilder: 1.2.2
    118     ChimeraX-ButtonPanel: 1.0.1
    119     ChimeraX-CageBuilder: 1.0.1
    120     ChimeraX-CellPack: 1.0
    121     ChimeraX-Centroids: 1.3.2
    122     ChimeraX-ChangeChains: 1.1
    123     ChimeraX-CheckWaters: 1.3.1
    124     ChimeraX-ChemGroup: 2.0.1
    125     ChimeraX-Clashes: 2.2.4
    126     ChimeraX-ColorActions: 1.0.3
    127     ChimeraX-ColorGlobe: 1.0
    128     ChimeraX-ColorKey: 1.5.4
    129     ChimeraX-CommandLine: 1.2.5
    130     ChimeraX-ConnectStructure: 2.0.1
    131     ChimeraX-Contacts: 1.0.1
    132     ChimeraX-Core: 1.7.dev202310231853
    133     ChimeraX-CoreFormats: 1.2
    134     ChimeraX-coulombic: 1.4.2
    135     ChimeraX-Crosslinks: 1.0
    136     ChimeraX-Crystal: 1.0
    137     ChimeraX-CrystalContacts: 1.0.1
    138     ChimeraX-DataFormats: 1.2.3
    139     ChimeraX-Dicom: 1.2
    140     ChimeraX-DistMonitor: 1.4
    141     ChimeraX-DockPrep: 1.1.2
    142     ChimeraX-Dssp: 2.0
    143     ChimeraX-EMDB-SFF: 1.0
    144     ChimeraX-ESMFold: 1.0
    145     ChimeraX-FileHistory: 1.0.1
    146     ChimeraX-FunctionKey: 1.0.1
    147     ChimeraX-Geometry: 1.3
    148     ChimeraX-gltf: 1.0
    149     ChimeraX-Graphics: 1.1.1
    150     ChimeraX-Hbonds: 2.4
    151     ChimeraX-Help: 1.2.2
    152     ChimeraX-HKCage: 1.3
    153     ChimeraX-IHM: 1.1
    154     ChimeraX-ImageFormats: 1.2
    155     ChimeraX-IMOD: 1.0
    156     ChimeraX-IO: 1.0.1
    157     ChimeraX-ItemsInspection: 1.0.1
    158     ChimeraX-IUPAC: 1.0
    159     ChimeraX-Label: 1.1.8
    160     ChimeraX-ListInfo: 1.2.1
    161     ChimeraX-Log: 1.1.6
    162     ChimeraX-LookingGlass: 1.1
    163     ChimeraX-Maestro: 1.9.1
    164     ChimeraX-Map: 1.1.4
    165     ChimeraX-MapData: 2.0
    166     ChimeraX-MapEraser: 1.0.1
    167     ChimeraX-MapFilter: 2.0.1
    168     ChimeraX-MapFit: 2.0
    169     ChimeraX-MapSeries: 2.1.1
    170     ChimeraX-Markers: 1.0.1
    171     ChimeraX-Mask: 1.0.2
    172     ChimeraX-MatchMaker: 2.1.2
    173     ChimeraX-MCopy: 1.0
    174     ChimeraX-MDcrds: 2.6
    175     ChimeraX-MedicalToolbar: 1.0.2
    176     ChimeraX-Meeting: 1.0.1
    177     ChimeraX-MLP: 1.1.1
    178     ChimeraX-mmCIF: 2.12.1
    179     ChimeraX-MMTF: 2.2
    180     ChimeraX-Modeller: 1.5.12
    181     ChimeraX-ModelPanel: 1.4
    182     ChimeraX-ModelSeries: 1.0.1
    183     ChimeraX-Mol2: 2.0.3
    184     ChimeraX-Mole: 1.0
    185     ChimeraX-Morph: 1.0.2
    186     ChimeraX-MouseModes: 1.2
    187     ChimeraX-Movie: 1.0
    188     ChimeraX-Neuron: 1.0
    189     ChimeraX-Nifti: 1.1
    190     ChimeraX-NIHPresets: 1.1.15
    191     ChimeraX-NRRD: 1.1
    192     ChimeraX-Nucleotides: 2.0.3
    193     ChimeraX-OpenCommand: 1.13
    194     ChimeraX-PDB: 2.7.2
    195     ChimeraX-PDBBio: 1.0.1
    196     ChimeraX-PDBLibrary: 1.0.2
    197     ChimeraX-PDBMatrices: 1.0
    198     ChimeraX-PhenixUI: 1.2.0
    199     ChimeraX-PickBlobs: 1.0.1
    200     ChimeraX-Positions: 1.0
    201     ChimeraX-PresetMgr: 1.1
    202     ChimeraX-PubChem: 2.1
    203     ChimeraX-ReadPbonds: 1.0.1
    204     ChimeraX-Registration: 1.1.2
    205     ChimeraX-RemoteControl: 1.0
    206     ChimeraX-RenderByAttr: 1.1
    207     ChimeraX-RenumberResidues: 1.1
    208     ChimeraX-ResidueFit: 1.0.1
    209     ChimeraX-RestServer: 1.2
    210     ChimeraX-RNALayout: 1.0
    211     ChimeraX-RotamerLibMgr: 4.0
    212     ChimeraX-RotamerLibsDunbrack: 2.0
    213     ChimeraX-RotamerLibsDynameomics: 2.0
    214     ChimeraX-RotamerLibsRichardson: 2.0
    215     ChimeraX-SaveCommand: 1.5.1
    216     ChimeraX-SchemeMgr: 1.0
    217     ChimeraX-SDF: 2.0.1
    218     ChimeraX-Segger: 1.0
    219     ChimeraX-Segment: 1.0.1
    220     ChimeraX-SelInspector: 1.0
    221     ChimeraX-SeqView: 2.11
    222     ChimeraX-Shape: 1.0.1
    223     ChimeraX-Shell: 1.0.1
    224     ChimeraX-Shortcuts: 1.1.1
    225     ChimeraX-ShowSequences: 1.0.2
    226     ChimeraX-SideView: 1.0.1
    227     ChimeraX-Smiles: 2.1.2
    228     ChimeraX-SmoothLines: 1.0
    229     ChimeraX-SpaceNavigator: 1.0
    230     ChimeraX-StdCommands: 1.12.2
    231     ChimeraX-STL: 1.0.1
    232     ChimeraX-Storm: 1.0
    233     ChimeraX-StructMeasure: 1.1.2
    234     ChimeraX-Struts: 1.0.1
    235     ChimeraX-Surface: 1.0.1
    236     ChimeraX-SwapAA: 2.0.1
    237     ChimeraX-SwapRes: 2.2.2
    238     ChimeraX-TapeMeasure: 1.0
    239     ChimeraX-TaskManager: 1.0
    240     ChimeraX-Test: 1.0
    241     ChimeraX-Toolbar: 1.1.2
    242     ChimeraX-ToolshedUtils: 1.2.4
    243     ChimeraX-Topography: 1.0
    244     ChimeraX-ToQuest: 1.0
    245     ChimeraX-Tug: 1.0.1
    246     ChimeraX-UI: 1.33.1
    247     ChimeraX-uniprot: 2.3
    248     ChimeraX-UnitCell: 1.0.1
    249     ChimeraX-ViewDockX: 1.3.2
    250     ChimeraX-VIPERdb: 1.0
    251     ChimeraX-Vive: 1.1
    252     ChimeraX-VolumeMenu: 1.0.1
    253     ChimeraX-VTK: 1.0
    254     ChimeraX-WavefrontOBJ: 1.0
    255     ChimeraX-WebCam: 1.0.2
    256     ChimeraX-WebServices: 1.1.2
    257     ChimeraX-Zone: 1.0.1
    258     colorama: 0.4.6
    259     comm: 0.1.4
    260     contourpy: 1.1.1
    261     cxservices: 1.2.2
    262     cycler: 0.12.1
    263     Cython: 0.29.33
    264     debugpy: 1.8.0
    265     decorator: 5.1.1
    266     docutils: 0.19
    267     executing: 2.0.0
    268     filelock: 3.9.0
    269     fonttools: 4.43.1
    270     funcparserlib: 1.0.1
    271     glfw: 2.6.2
    272     grako: 3.16.5
    273     h5py: 3.10.0
    274     html2text: 2020.1.16
    275     idna: 3.4
    276     ihm: 0.38
    277     imagecodecs: 2023.9.18
    278     imagesize: 1.4.1
    279     ipykernel: 6.23.2
    280     ipython: 8.14.0
    281     ipython-genutils: 0.2.0
    282     ipywidgets: 8.1.1
    283     jedi: 0.18.2
    284     Jinja2: 3.1.2
    285     jupyter-client: 8.2.0
    286     jupyter-core: 5.4.0
    287     jupyterlab-widgets: 3.0.9
    288     kiwisolver: 1.4.5
    289     line-profiler: 4.0.2
    290     lxml: 4.9.2
    291     lz4: 4.3.2
    292     MarkupSafe: 2.1.3
    293     matplotlib: 3.7.2
    294     matplotlib-inline: 0.1.6
    295     msgpack: 1.0.4
    296     nest-asyncio: 1.5.8
    297     netCDF4: 1.6.2
    298     networkx: 3.1
    299     nibabel: 5.0.1
    300     nptyping: 2.5.0
    301     numexpr: 2.8.7
    302     numpy: 1.25.1
    303     openvr: 1.23.701
    304     packaging: 21.3
    305     ParmEd: 3.4.3
    306     parso: 0.8.3
    307     pep517: 0.13.0
    308     pexpect: 4.8.0
    309     pickleshare: 0.7.5
    310     Pillow: 10.0.1
    311     pip: 23.0
    312     pkginfo: 1.9.6
    313     platformdirs: 3.11.0
    314     prompt-toolkit: 3.0.39
    315     psutil: 5.9.5
    316     ptyprocess: 0.7.0
    317     pure-eval: 0.2.2
    318     py-cpuinfo: 9.0.0
    319     pycollada: 0.7.2
    320     pydicom: 2.3.0
    321     Pygments: 2.16.1
    322     pynrrd: 1.0.0
    323     PyOpenGL: 3.1.7
    324     PyOpenGL-accelerate: 3.1.7
    325     pyopenxr: 1.0.2801
    326     pyparsing: 3.0.9
    327     pyproject-hooks: 1.0.0
    328     PyQt6: 6.3.1
    329     PyQt6-Qt6: 6.3.2
    330     PyQt6-sip: 13.4.0
    331     PyQt6-WebEngine: 6.3.1
    332     PyQt6-WebEngine-Qt6: 6.3.2
    333     python-dateutil: 2.8.2
    334     pytz: 2023.3.post1
    335     pyzmq: 25.1.1
    336     qtconsole: 5.4.3
    337     QtPy: 2.4.0
    338     RandomWords: 0.4.0
    339     requests: 2.31.0
    340     scipy: 1.11.1
    341     setuptools: 67.4.0
    342     setuptools-scm: 7.0.5
    343     sfftk-rw: 0.7.3
    344     six: 1.16.0
    345     snowballstemmer: 2.2.0
    346     sortedcontainers: 2.4.0
    347     soupsieve: 2.5
    348     sphinx: 6.1.3
    349     sphinx-autodoc-typehints: 1.22
    350     sphinxcontrib-applehelp: 1.0.7
    351     sphinxcontrib-blockdiag: 3.0.0
    352     sphinxcontrib-devhelp: 1.0.5
    353     sphinxcontrib-htmlhelp: 2.0.4
    354     sphinxcontrib-jsmath: 1.0.1
    355     sphinxcontrib-qthelp: 1.0.6
    356     sphinxcontrib-serializinghtml: 1.1.9
    357     stack-data: 0.6.3
    358     superqt: 0.5.0
    359     tables: 3.8.0
    360     tcia-utils: 1.5.1
    361     tifffile: 2023.7.18
    362     tinyarray: 1.2.4
    363     tomli: 2.0.1
    364     tornado: 6.3.3
    365     traitlets: 5.9.0
    366     typing-extensions: 4.8.0
    367     tzdata: 2023.3
    368     urllib3: 2.0.7
    369     wcwidth: 0.2.8
    370     webcolors: 1.12
    371     wheel: 0.38.4
    372     wheel-filename: 1.4.1
    373     widgetsnbextension: 4.0.9
    374 
    375 }}}
     14Best,
     15James