Opened 3 years ago

Closed 3 years ago

#7310 closed defect (not a bug)

~tile / tile off not in 1.3?

Reported by: andrey.malyutin@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Structure Comparison Version:
Keywords: Cc: Elaine Meng
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Hello,
Per description of the "tile" command here: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/tile.html , "~tile" and "tile off" do not work.  I get "unknown command" error in the log.  Perhaps they work only in version 1.4+ ? 
Thank you.

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/andrey.malyutin/Library/CloudStorage/OneDrive-
> Takeda/Documents/Projects/Integrins/Data/H12/Maps/Int12_H12_H-G2_070122/J512_C3D/cryosparc_P25_J521_00088_volume_series/cryosparc_P25_J521_class_00_00088_volume.mrc

Opened cryosparc_P25_J521_class_00_00088_volume.mrc as #1, grid size
192,192,192, pixel 1.85, shown at level 0.104, step 1, values float32  

> volume #1 level 0.3234

> open /Users/andrey.malyutin/Library/CloudStorage/OneDrive-
> Takeda/Documents/Projects/Integrins/Data/H12/Maps/Int12_H12_H-G2_070122/J512_C3D/cryosparc_P25_J521_00088_volume_series/cryosparc_P25_J521_class_01_00088_volume.mrc

Opened cryosparc_P25_J521_class_01_00088_volume.mrc as #2, grid size
192,192,192, pixel 1.85, shown at level 0.103, step 1, values float32  

> open /Users/andrey.malyutin/Library/CloudStorage/OneDrive-
> Takeda/Documents/Projects/Integrins/Data/H12/Maps/Int12_H12_H-G2_070122/J512_C3D/cryosparc_P25_J521_00088_volume_series/cryosparc_P25_J521_class_02_00088_volume.mrc

Opened cryosparc_P25_J521_class_02_00088_volume.mrc as #3, grid size
192,192,192, pixel 1.85, shown at level 0.101, step 1, values float32  

> open /Users/andrey.malyutin/Library/CloudStorage/OneDrive-
> Takeda/Documents/Projects/Integrins/Data/H12/Maps/Int12_H12_H-G2_070122/J512_C3D/cryosparc_P25_J521_00088_volume_series/cryosparc_P25_J521_class_03_00088_volume.mrc

Opened cryosparc_P25_J521_class_03_00088_volume.mrc as #4, grid size
192,192,192, pixel 1.85, shown at level 0.106, step 1, values float32  

> open /Users/andrey.malyutin/Library/CloudStorage/OneDrive-
> Takeda/Documents/Projects/Integrins/Data/H12/Maps/Int12_H12_H-G2_070122/J512_C3D/cryosparc_P25_J521_00088_volume_series/cryosparc_P25_J521_class_04_00088_volume.mrc

Opened cryosparc_P25_J521_class_04_00088_volume.mrc as #5, grid size
192,192,192, pixel 1.85, shown at level 0.104, step 1, values float32  

> open /Users/andrey.malyutin/Library/CloudStorage/OneDrive-
> Takeda/Documents/Projects/Integrins/Data/H12/Maps/Int12_H12_H-G2_070122/J512_C3D/cryosparc_P25_J521_00088_volume_series/cryosparc_P25_J521_class_05_00088_volume.mrc

Opened cryosparc_P25_J521_class_05_00088_volume.mrc as #6, grid size
192,192,192, pixel 1.85, shown at level 0.102, step 1, values float32  

> open /Users/andrey.malyutin/Library/CloudStorage/OneDrive-
> Takeda/Documents/Projects/Integrins/Data/H12/Maps/Int12_H12_H-G2_070122/J512_C3D/cryosparc_P25_J521_00088_volume_series/cryosparc_P25_J521_class_06_00088_volume.mrc

Opened cryosparc_P25_J521_class_06_00088_volume.mrc as #7, grid size
192,192,192, pixel 1.85, shown at level 0.106, step 1, values float32  

> open /Users/andrey.malyutin/Library/CloudStorage/OneDrive-
> Takeda/Documents/Projects/Integrins/Data/H12/Maps/Int12_H12_H-G2_070122/J512_C3D/cryosparc_P25_J521_00088_volume_series/cryosparc_P25_J521_class_07_00088_volume.mrc

Opened cryosparc_P25_J521_class_07_00088_volume.mrc as #8, grid size
192,192,192, pixel 1.85, shown at level 0.101, step 1, values float32  

> open /Users/andrey.malyutin/Library/CloudStorage/OneDrive-
> Takeda/Documents/Projects/Integrins/Data/H12/Maps/Int12_H12_H-G2_070122/J512_C3D/cryosparc_P25_J521_00088_volume_series/cryosparc_P25_J521_class_08_00088_volume.mrc

Opened cryosparc_P25_J521_class_08_00088_volume.mrc as #9, grid size
192,192,192, pixel 1.85, shown at level 0.105, step 1, values float32  

> open /Users/andrey.malyutin/Library/CloudStorage/OneDrive-
> Takeda/Documents/Projects/Integrins/Data/H12/Maps/Int12_H12_H-G2_070122/J512_C3D/cryosparc_P25_J521_00088_volume_series/cryosparc_P25_J521_class_09_00088_volume.mrc

Opened cryosparc_P25_J521_class_09_00088_volume.mrc as #10, grid size
192,192,192, pixel 1.85, shown at level 0.104, step 1, values float32  

> volume #1-10 level 0.3

> tile

10 models tiled  

> volume #1 level 0.303

> volume #5 level 0.303

> volume #10 level 0.3346

> volume #9 level 0.3104

> volume #4 level 0.4157

> volume #1 level 0.3274

> volume #4 level 0.3187

> volume #5 level 0.3938

> volume #10 level 0.2377

> untile

Unknown command: untile  

> ~tile

Unknown command: ~tile  

> reset

Unknown command: reset  

> revert

Unknown command: revert  

> view

> view orient

> tile off

Expected a models specifier or a keyword  

> tile off #1-10

Expected a models specifier or a keyword  

> tile #1-10 off

Expected a keyword  

> ~tile

Unknown command: ~tile  

> tile

10 models tiled  

> tile off

Expected a models specifier or a keyword  

> undo

> tile off #1

Expected a models specifier or a keyword  

> tile off volume #1-10

Expected a models specifier or a keyword  

> tileoff #1-10

Unknown command: tileoff #1-10  

> ~tile volume #1-10

Unknown command: ~tile volume #1-10  

> help tile




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1
OpenGL vendor: AppleHardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro17,1
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache: 8 MB
      Memory: 16 GB

Software:

    System Software Overview:

      System Version: macOS 12.4 (21F79)
      Kernel Version: Darwin 21.5.0
      Time since boot: 6 days 22:57

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        S34J55x:
          Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
          UI Looks like: 3440 x 1440 @ 50.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    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-Clipper: 0.17.0
    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: 1.3
    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-ISOLDE: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    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: 1.13.7
    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
    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
    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: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.3
    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: 1.11.3
    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
    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

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Cc: Elaine Meng added
Component: Unassigned → Structure Comparison
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ~tile / tile off not in 1.3?

comment:2 by Elaine Meng, 3 years ago

Resolution: → not a bug
Status: assigned → closed

As you suspected, version 1.3 does not have "tile off" -- if you look at the documentation included with the 1.3 download (e.g. command "help tile" when you are using 1.3) it will show the corresponding state of the command, which does not include "tile off", sorry. The documentation also mentions that you can reverse it with "undo". However, I understand that may not be convenient if you did several other things between the tile and when you wanted to reverse it. Otherwise the workaround is to use version 1.4 if possible.

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