Surface coloring

[laura.rigobello@…]

The following bug report has been submitted:
Platform:        macOS-14.5-arm64-arm-64bit
ChimeraX Version: 1.8rc202405230136 (2024-05-23 01:36:41 UTC)
Description
The surface of a molecule has a different color than the color of the Atoms/Bonds representation (in this case, the Atoms/Bonds representation is blue and magenta, while the surface is green).

OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,7
      Model Number: Z16S000EBT/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.121.1
      OS Loader Version: 10151.121.1

Software:

    System Software Overview:

      System Version: macOS 14.5 (23F79)
      Kernel Version: Darwin 23.5.0
      Time since boot: 7 days, 32 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        LF24T35:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 75.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57
    ChimeraX-AtomicLibrary: 14.0.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
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    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.4
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8rc202405230136
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
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    ChimeraX-MMTF: 2.2
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    ChimeraX-ModelPanel: 1.5
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    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
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    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.4
    ChimeraX-PDB: 2.7.5
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    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.10
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
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    executing: 2.0.1
    filelock: 3.13.4
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    funcparserlib: 2.0.0a0
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    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
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    imagecodecs: 2024.1.1
    imagesize: 1.4.1
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File attachment: Screenshot 2024-05-31 at 10.04.14.png

Screenshot 2024-05-31 at 10.04.14.png​

[laura.rigobello@…]

Added by email2trac

[pett]

Hi Laura,

Is that a molecular surface in your image (i.e. generated with the "surface" command or Actions→Surface)? Most ways of coloring affect both atoms and their surface. For instance the "color" command affects both unless you provide a "target" keyword. The Color Actions tool you are showing in your image will affect both when you have both "Atoms/Bonds" and "Surfaces" checked (which is the default). If in the image you were to click "Forest Green", both the atoms and the surface should change to that color. So what process did you use to get the colors you have in the image?
Also, again assuming that's a molecular surface, "color fromatoms" will color the surface to match the atoms.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[laura.rigobello@…]

Hi,

In the photo sent to you, I have colored the nuclotides with different colors (none of them in green) with the command color. Then, I was trying to show the surface of some nucleotides. I have tried both ways (I have used the command surface and I have clicked on the surface tool in the Action dropdown menu), but in both cases the surface was green and not with the color of the Atoms/Bonds representation. I checked the color options and there were the default parameters. That is the reason why I was wondering it was a bug.

So to color the surface at the same way as the Atoms/Bonds representation, I have to use the command color fromatoms?

Thanks for your attention.

Best regards,
Laura

________________________________
Da: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Inviato: venerdì 31 maggio 2024 19:48
A: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Laura Rigobello - laura.rigobello@studio.unibo.it <laura.rigobello@studio.unibo.it>
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; meng@cgl.ucsf.edu <meng@cgl.ucsf.edu>
Oggetto: Re: [ChimeraX] #15347: Surface coloring

#15347: Surface coloring
----------------------------------------+----------------------
          Reporter:  laura.rigobello@…  |      Owner:  pett
              Type:  defect             |     Status:  accepted
          Priority:  normal             |  Milestone:
         Component:  Depiction          |    Version:
        Resolution:                     |   Keywords:
        Blocked By:                     |   Blocking:
Notify when closed:                     |   Platform:  all
           Project:  ChimeraX           |
----------------------------------------+----------------------
Comment (by pett):

 Hi Laura,
         Is that a molecular surface in your image (i.e. generated with the
 "surface" command or Actions→Surface)?  Most ways of coloring affect both
 atoms and their surface.  For instance the "color" command affects both
 unless you provide a "target" keyword.  The Color Actions tool you are
 showing in your image will affect both when you have both "Atoms/Bonds"
 and "Surfaces" checked (which is the default).  If in the image you were
 to click "Forest Green", both the atoms and the surface should change to
 that color.  So what process did you use to get the colors you have in the
 image?
         Also, again assuming that's a molecular surface, "color fromatoms"
 will color the surface to match the atoms.

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/15347#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Elaine Meng]

It is because you created the surface after you did the coloring.  The first time you use show surface (menu or command) it creates the surface.  When it creates the surface it makes the whole chain surface the same color.  Probably the greenish color is the average of all the colors of the residues in that chain.

However, if you show the surface before you do the residue coloring, then when you color the residue atoms it includes the surface for those atoms and colors them the same way.  So just show the whole surface first.  Then you can hide the whole surface before doing the residue coloring if you want and then show it after the residue coloring is done.  It will match the residues because it already existed before you did the coloring.

[laura.rigobello@…]

Now it is clear! Thank you very much for your answer.

Best regards,
Laura

Inviato da Outlook per iOS<https://aka.ms/o0ukef>
________________________________
Da: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Inviato: Monday, June 3, 2024 8:20:08 PM
A: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Laura Rigobello - laura.rigobello@studio.unibo.it <laura.rigobello@studio.unibo.it>
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; meng@cgl.ucsf.edu <meng@cgl.ucsf.edu>
Oggetto: Re: [ChimeraX] #15347: Surface coloring

#15347: Surface coloring
----------------------------------------+--------------------
          Reporter:  laura.rigobello@…  |      Owner:  pett
              Type:  defect             |     Status:  closed
          Priority:  normal             |  Milestone:
         Component:  Depiction          |    Version:
        Resolution:  not a bug          |   Keywords:
        Blocked By:                     |   Blocking:
Notify when closed:                     |   Platform:  all
           Project:  ChimeraX           |
----------------------------------------+--------------------
Changes (by pett):

 * resolution:   => not a bug
 * status:  accepted => closed

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/15347#comment:7>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker