color byattribute range option gives wrong range when palette is alphafold

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.11.dev202508252314 (2025-08-25 23:14:16 UTC)
Description
Specifying range option in color bfactor command with palette alphafold does not correctly use the range.  Probably this is due to a bug handling range where the palette has a default range, in the case of the alphafold palette that default is from 0 to 100.

Log:
UCSF ChimeraX version: 1.11.dev202508252314 (2025-08-25)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Installed ChimeraX-PhenixUI (1.3.9)  

> open
> /Users/goddard/Desktop/boltz/boltz_9gqu_1/boltz_results_9gqu/predictions/9gqu/9gqu_model_0.cif
> format mmcif logInfo false

> color bfactor palette alphafold

4768 atoms, 507 residues, atom bfactor range 40.1 to 97.9  

> color bfactor palette alphafold range 40,100

4768 atoms, 507 residues, atom bfactor range 40.1 to 97.9  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2 Ultra
OpenGL vendor: Apple

Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PySide6 6.9.2, Qt 6.9.2
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac Studio
      Model Identifier: Mac14,14
      Model Number: Z1800003VLL/A
      Chip: Apple M2 Ultra
      Total Number of Cores: 24 (16 performance and 8 efficiency)
      Memory: 64 GB
      System Firmware Version: 11881.140.96
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.6.1 (24G90)
      Kernel Version: Darwin 24.6.0
      Time since boot: 22 days, 17 hours, 2 minutes

Graphics/Displays:

    Apple M2 Ultra:

      Chipset Model: Apple M2 Ultra
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 60
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        PHL 278B1:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


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[Tom Goddard]

Fixed.

The command "color bfactor palette alphafold range 40,100" now maps the given value range of 40 to 100 to the red-yellow-orange-blue colors of the alphafold palette. If the range option were not specified the range 0-100 is the default for the alphafold palette. The colors in the alphafold color map are not equally spaced. When the range is specified that unequal spacing is preserved. The current values associated with each color (0 to 100) are linearly scaled to fit the range 40 to 100 in the example.

I don't think it makes sense to give the range option with the alphafold colormap since the spacing and default values associated with the colors are meant to be a standard coloring. But if a user does decide to use the range option I think the above behavior is the most sensible.