Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#5125 closed enhancement (wontfix)

RFE: scroll contour

Reported by: jaremko@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc:
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.dev202107210242 (2021-07-21 02:42:36 UTC)
Description
Add feature that allows you to scroll the contour when the mouser is hovering over the contour histogram.  This feature already works for the morph slider,  so I figure this can be implemented in the contour histogram.

Log:
> ui mousemode right zoom

> set bgColor white

> graphics silhouettes true

> graphics silhouettes width 3

> hide all atoms

> style stick

Changed 0 atom styles  

> style ions sphere

Changed 0 atom styles  

> style ions sphere

Changed 0 atom styles  

> show all cartoons

> show ligand target ab

> show ions atoms

> show sidechain & (ligand | ions) :< 3.5 target ab

> color /a #55c087

> color /b #ffe255

> color /c #f6986c

> color /d #6b80bc

> color /e #aa7fba

> color /g #FFC0CB

> color /h #b2b2b2

> color /i red

> color byhetero

> lighting soft

> lighting depthCue false

> cartoon suppressBackboneDisplay false

> volume fastEncloseVolume 80000

Error running startup command 'vol fastEncloseVolume 80000': No volumes
specified  
UCSF ChimeraX version: 1.3.dev202107210242 (2021-07-21)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/jaremko/Documents/cryoem/2021-08-26_x138-Hs128-Nuc200/P146/J4/cryosparc_P146_J4_class_01_final_volume.mrc

Opened cryosparc_P146_J4_class_01_final_volume.mrc as #1, grid size
192,192,192, pixel 2.38, shown at level 0.131, step 1, values float32  

> open
> /Users/jaremko/Documents/cryoem/2021-08-26_x138-Hs128-Nuc200/P146/J4/cryosparc_P146_J4_class_02_final_volume.mrc

Opened cryosparc_P146_J4_class_02_final_volume.mrc as #2, grid size
192,192,192, pixel 2.38, shown at level 0.129, step 1, values float32  

> open
> /Users/jaremko/Documents/cryoem/2021-08-26_x138-Hs128-Nuc200/P146/J4/cryosparc_P146_J4_class_03_final_volume.mrc

Opened cryosparc_P146_J4_class_03_final_volume.mrc as #3, grid size
192,192,192, pixel 2.38, shown at level 0.128, step 1, values float32  

> open
> /Users/jaremko/Documents/cryoem/2021-08-26_x138-Hs128-Nuc200/P146/J4/cryosparc_P146_J4_class_04_final_volume.mrc

Opened cryosparc_P146_J4_class_04_final_volume.mrc as #4, grid size
192,192,192, pixel 2.38, shown at level 0.128, step 1, values float32  

> tile

4 models tiled  

> volume #1 level 0.2303

> volume #2 level 0.2677

> volume #3 level 0.2535

> volume #4 level 0.2523

> volume #2 level 0.3443

> close session

> open
> /Users/jaremko/Documents/cryoem/2021-08-26_x138-Hs128-Nuc200/P146/J9/cryosparc_P146_J9_class_00_00222_volume.mrc

Opened cryosparc_P146_J9_class_00_00222_volume.mrc as #1, grid size 84,84,84,
pixel 5.45, shown at level 0.168, step 1, values float32  

> open
> /Users/jaremko/Documents/cryoem/2021-08-26_x138-Hs128-Nuc200/P146/J9/cryosparc_P146_J9_class_01_00222_volume.mrc

Opened cryosparc_P146_J9_class_01_00222_volume.mrc as #2, grid size 84,84,84,
pixel 5.45, shown at level 0.386, step 1, values float32  

> open
> /Users/jaremko/Documents/cryoem/2021-08-26_x138-Hs128-Nuc200/P146/J9/cryosparc_P146_J9_class_02_00222_volume.mrc

Opened cryosparc_P146_J9_class_02_00222_volume.mrc as #3, grid size 84,84,84,
pixel 5.45, shown at level 0.342, step 1, values float32  

> open
> /Users/jaremko/Documents/cryoem/2021-08-26_x138-Hs128-Nuc200/P146/J9/cryosparc_P146_J9_class_03_00222_volume.mrc

Opened cryosparc_P146_J9_class_03_00222_volume.mrc as #4, grid size 84,84,84,
pixel 5.45, shown at level 0.732, step 1, values float32  

> open
> /Users/jaremko/Documents/cryoem/2021-08-26_x138-Hs128-Nuc200/P146/J9/cryosparc_P146_J9_class_04_00222_volume.mrc

Opened cryosparc_P146_J9_class_04_00222_volume.mrc as #5, grid size 84,84,84,
pixel 5.45, shown at level 0.291, step 1, values float32  

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> volume #1 level 1.383

> volume #2 level 0.2664

> volume #2 level 0.9959

> volume #3 level 0.3588

> volume #4 level 0.05074

> volume #4 level 0.3107

> volume #5 level 0.2057

> volume #2 level 0.4004

> volume #3 level 0.2377

> volume #3 level 0.5491

> volume #1 level 0.1678

> volume #1 level 0.1808

> volume #1 level 0.1155

> volume #1 level 0.1808

> close session

> open
> /Users/jaremko/Documents/cryoem/2021-08-26_x138-Hs128-Nuc200/P146/J12/cryosparc_P146_J12_cluster_001.mrc

Opened cryosparc_P146_J12_cluster_001.mrc as #1, grid size 416,416,416, pixel
1.1, shown at level 0.00656, step 2, values float32  

> open
> /Users/jaremko/Documents/cryoem/2021-08-26_x138-Hs128-Nuc200/P146/J12/cryosparc_P146_J12_cluster_002.mrc

Opened cryosparc_P146_J12_cluster_002.mrc as #2, grid size 416,416,416, pixel
1.1, shown at level 0.0067, step 2, values float32  

> close session

> open
> /Users/jaremko/Documents/cryoem/2021-08-26_x138-Hs128-Nuc200/P146/J12/cryosparc_P146_J12_cluster_000.mrc

Opened cryosparc_P146_J12_cluster_000.mrc as #1, grid size 416,416,416, pixel
1.1, shown at level 0.00664, step 2, values float32  

> open
> /Users/jaremko/Documents/cryoem/2021-08-26_x138-Hs128-Nuc200/P146/J12/cryosparc_P146_J12_cluster_001.mrc

Opened cryosparc_P146_J12_cluster_001.mrc as #2, grid size 416,416,416, pixel
1.1, shown at level 0.00656, step 2, values float32  

> open
> /Users/jaremko/Documents/cryoem/2021-08-26_x138-Hs128-Nuc200/P146/J12/cryosparc_P146_J12_cluster_002.mrc

Opened cryosparc_P146_J12_cluster_002.mrc as #3, grid size 416,416,416, pixel
1.1, shown at level 0.0067, step 2, values float32  

> volume all step 1

> hide #!3 models

> hide #!2 models

> volume #3 level 0.03389

> volume #1 level 0.005372

> volume #1 level 0.02062

> volume #2 level 0.005621

> volume #2 level 0.006556

> volume #3 level 0.004115

> volume morph #1,2

Opened morph as #4, grid size 416,416,416, pixel 1.1, shown at step 1, values
float32  

> volume #4 level 0.007524

> volume #4 level 0.1001

> volume morph #1,3

Opened morph as #5, grid size 416,416,416, pixel 1.1, shown at step 1, values
float32  

> volume #5 level 0.1565

> volume #5 level 0.005845

> volume #4 level 0.005662

> volume #4 level 0.008468




OpenGL version: 4.1 ATI-4.5.14
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 1554.120.19.0.0 (iBridge: 18.16.14663.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 11.4 (20F71)
      Kernel Version: Darwin 20.5.0
      Time since boot: 16 days 18:59

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-020
      Option ROM Version: 113-D32206U1-020
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          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: 1.5.0
    chardet: 4.0.0
    charset-normalizer: 2.0.3
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AltlocExplorer: 1.0
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.26.1
    ChimeraX-AtomicLibrary: 3.4
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    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: 1.3.2
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202107210242
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.4
    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
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    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: 1.2.1
    ChimeraX-MDcrds: 2.4
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.2
    ChimeraX-ModelPanel: 1.1
    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: 1.6.2
    ChimeraX-PDB: 2.4.4
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    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
    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: 1.4.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.1
    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
    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: 1.10.1
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    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
    comtypes: 1.1.10
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.23
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.3.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.20
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 2.11.3
    jupyter-client: 6.1.12
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 1.1.1
    matplotlib: 3.4.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.2
    netCDF4: 1.5.6
    networkx: 2.5.1
    numexpr: 2.7.3
    numpy: 1.21.0
    numpydoc: 1.1.0
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.2
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.2.0
    pip: 21.1.1
    pkginfo: 1.7.0
    prompt-toolkit: 3.0.19
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.9.0
    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: 22.1.0
    qtconsole: 5.1.0
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    RandomWords: 0.3.0
    requests: 2.25.1
    scipy: 1.6.3
    setuptools: 57.0.0
    sfftk-rw: 0.7.0.post1
    six: 1.16.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.4.0
    Sphinx: 4.0.1
    sphinxcontrib-applehelp: 1.0.2
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    sphinxcontrib-devhelp: 1.0.2
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    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
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    traitlets: 5.0.5
    urllib3: 1.26.6
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.2
    wheel-filename: 1.3.0

Change History (3)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → RFE: scroll contour
Type: defect → enhancement

Requested by Matt Jaremko

comment:2 by Tom Goddard, 4 years ago

Resolution: → wontfix
Status: assigned → closed

It's a nice idea. But the Volume panel itself scrolls when several volumes are open since they do not all fit in the panel. Making scroll adjust the contour level would make the panel scrolling not work. So it does not seem feasible to do that.

in reply to:  3 ; comment:3 by jaremko@…, 4 years ago 

Alright, that makes sense. thanks

Matt
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