Make mutation score residue coloring use gray for unassociated residues

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-26.5.2-arm64-arm-64bit
ChimeraX Version: 1.13.dev202607062341 (2026-07-06 23:41:36 UTC)
Description
Mutation score coloring of a structure colors unassociated residues white which is also used in the default red-white-blue color map making it impossible to see which residues have no score.  Change the color for residues with no score to gray.

Log:
UCSF ChimeraX version: 1.13.dev202607062341 (2026-07-06)  
© 2016-2026 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open P38398 format mmcif fromDatabase alphafold

Chain information for AlphaFold P38398 #1  
---  
Chain | Description | UniProt  
A | Breast cancer type 1 susceptibility protein | BRCA1_HUMAN 1-1863  
  
Color AlphaFold P38398 by residue attribute pLDDT_score  

> open /Users/goddard/Downloads/urn_mavedb_00001222-b-2_scores.csv format ms

Summary of feedback from opening
/Users/goddard/Downloads/urn_mavedb_00001222-b-2_scores.csv  
---  
note | Ignored 121 variants: 121 stop codons p.Ser1Ter, p.Pro3Ter, p.Ser4Ter ...  
  
Opened deep mutational scan data for 2150 mutations of 286 residues with score
names control_rep1_score, control_rep2_score, control_rep3_score,
control_rep4_score, control_score, control_std, control_var, rep1_score,
rep2_score, rep3_score, rep4_score, score, std, var.  
There are no structures associated with mutations
urn_mavedb_00001222-b-2_scores  

> mutationscores structure /A alignSequences true

Associated 1 chain to mutation set urn_mavedb_00001222-b-2_scores.  
Associated 286 residues of chain /A with 1 amino acid mismatch (S1613G).  

> mutationscores define mutation_score fromScoreName score combine mean

Defined score mutation_score having range -2.06 to 0.327 for 286 residues
using 2150 mutations  
Set attribute mutation_score for 286 residues of chain #1/A  

> color byattribute r:mutation_score #1/A palette
> -1.19,blue:-0.592,white:0.000746,white:0.594,red noValueColor white

14550 atoms, 1863 residues, atom mutation_score range -2.06 to 0.327  




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M2 Ultra
OpenGL vendor: Apple

Python: 3.11.15
Locale: en_US.UTF-8
Qt version: PySide6 6.11.1, Qt 6.11.1
Qt runtime version: 6.11.1
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: 18000.121.3
      OS Loader Version: 18000.121.3

Software:

    System Software Overview:

      System Version: macOS 26.5.2 (25F84)
      Kernel Version: Darwin 25.5.0
      Time since boot: 9 days, 32 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 4
      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]

Done.