mutationscores define does not clear pre-existing residue values

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-26.3.1-arm64-arm-64bit
ChimeraX Version: 1.12.dev202603101758 (2026-03-10 17:58:10 UTC)
Description
The mutationscores define command does not clear pre-existing residue values for the given attribute name.

Log:
UCSF ChimeraX version: 1.12.dev202603101758 (2026-03-10)  
© 2016-2026 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/goddard/ucsf/people/howard/lilace_scores_wide_all.csv format ms

Summary of feedback from opening
/Users/goddard/ucsf/people/howard/lilace_scores_wide_all.csv  
---  
note | Plotted 7827 mutations with effect_Buprenorphine on x-axis and effect_C6guano on y-axis  
  
Opened deep mutational scan data for 7830 mutations of 399 residues with score
names effect_Buprenorphine, effect_C6guano, effect_DAMGO, effect_FSK,
effect_Morphine, effect_Naloxone, effect_PZM21, effect_TRV130,
effect_carfentanil, effect_fentanyl, effect_mitragynine, effect_surface, pos.  

> open 8ef5 format mmcif fromDatabase pdb

8ef5 title:  
Fentanyl-bound mu-opioid receptor-Gi complex [more info...]  
  
Chain information for 8ef5 #1  
---  
Chain | Description | UniProt  
A F | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN 1-354  
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_RAT 2-340  
C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_BOVIN 1-68  
E | scFv16 |   
M R | Mu-type opioid receptor | OPRM_HUMAN 2-368  
  
Non-standard residues in 8ef5 #1  
---  
7V7 — N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide  
CLR — cholesterol  
  
Mutation set lilace_scores_wide_all has 2 associated chains #1/M,R.  

> mutationscores define mutation_score fromScoreName effect_Buprenorphine
> combine count

Defined score mutation_score having range 18 to 20 for 399 residues using 7827
mutations  
Set attribute mutation_score for 575 residues of chain #1/M,R  

> color byattribute r:mutation_score #1/M,R palette
> 18.6,blue:19.3,white:20,white:20.6,red noValueColor white

4954 atoms, 587 residues, atom mutation_score range 18 to 20  

> ui tool show "Render/Select by Attribute"

> select clear

> select /M-R:233

16 atoms, 14 bonds, 2 residues, 1 model selected  

> mutationscores define mutation_score fromScoreName effect_Buprenorphine
> combine count ranges "effect_Buprenorphine >= 0.646 and effect_Buprenorphine
> <= 0.723 and effect_C6guano >= 0.137 and effect_C6guano <= 0.3"

Defined score mutation_score having range 1 to 1 for 1 residues using 1
mutations  
Set attribute mutation_score for 2 residues of chain #1/M,R  

> color byattribute r:mutation_score #1/M,R palette
> 1,blue:1,white:1,white:1,red noValueColor white

4954 atoms, 587 residues, atom mutation_score range 1 to 1  

> ui tool show "Render/Select by Attribute"

Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_color_history.py", line 287, in
_show_render_by_attribute_gui  
_show_render_by_attribute_panel(self.session, mset, attr_name, palette)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_color_history.py", line 305, in
_show_render_by_attribute_panel  
rba_gui.configure(models = models, target = 'residues', tab = 'render',
attr_name = attribute_name,  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 485, in configure  
cur_min, cur_max, data = histogram.data_source  
^^^^^^^^^^^^^^^^^^^^^^  
ValueError: too many values to unpack (expected 3)  
  
ValueError: too many values to unpack (expected 3)  
  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 485, in configure  
cur_min, cur_max, data = histogram.data_source  
^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> select /M-R:114,122,165,233,249

76 atoms, 66 bonds, 10 residues, 1 model selected  

> mutationscores define mutation_score fromScoreName effect_Buprenorphine
> combine count ranges "effect_Buprenorphine >= 0.519 and effect_Buprenorphine
> <= 0.865 and effect_C6guano >= -0.174 and effect_C6guano <= 0.412"

Defined score mutation_score having range 1 to 1 for 5 residues using 5
mutations  
Set attribute mutation_score for 10 residues of chain #1/M,R  

> color byattribute r:mutation_score #1/M,R palette
> 1,blue:1,white:1,white:1,red noValueColor white

4954 atoms, 587 residues, atom mutation_score range 1 to 1  

> ui tool show "Render/Select by Attribute"

Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_color_history.py", line 287, in
_show_render_by_attribute_gui  
_show_render_by_attribute_panel(self.session, mset, attr_name, palette)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_color_history.py", line 305, in
_show_render_by_attribute_panel  
rba_gui.configure(models = models, target = 'residues', tab = 'render',
attr_name = attribute_name,  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 485, in configure  
cur_min, cur_max, data = histogram.data_source  
^^^^^^^^^^^^^^^^^^^^^^  
ValueError: too many values to unpack (expected 3)  
  
ValueError: too many values to unpack (expected 3)  
  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 485, in configure  
cur_min, cur_max, data = histogram.data_source  
^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> select
> /R,M:73,77,88,99-100,111-116,118,125,135,144,149,152,154,157-158,160-161,163-165,167-168,170-171,173-175,177-178,180-181,183,186,188,190,195,197,200,202-203,246,249,257-258,260-261,277,280,284,289,291,295,297-299,325,327-328,332-333,344

1076 atoms, 1028 bonds, 132 residues, 1 model selected  

> mutationscores define mutation_score fromScoreName effect_Buprenorphine
> combine count ranges "effect_Buprenorphine >= 0.272 and effect_Buprenorphine
> <= 0.742 and effect_C6guano >= 0.219 and effect_C6guano <= 0.931"

Defined score mutation_score having range 1 to 9 for 66 residues using 135
mutations  
Set attribute mutation_score for 132 residues of chain #1/M,R  

> color byattribute r:mutation_score #1/M,R palette
> -1.55,blue:0.848,white:3.24,white:5.64,red noValueColor white

4954 atoms, 587 residues, atom mutation_score range 1 to 9  

> ui tool show "Render/Select by Attribute"




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

Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PySide6 6.10.1, Qt 6.10.1
Qt runtime version: 6.10.1
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: 13822.81.10
      OS Loader Version: 13822.81.10

Software:

    System Software Overview:

      System Version: macOS 26.3.1 (a) (25D771280a)
      Kernel Version: Darwin 25.3.0
      Time since boot: 7 days, 14 hours, 58 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


Installed Packages:
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    build: 1.3.0
    certifi: 2025.8.3
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    ChimeraX-AtomicLibrary: 14.4
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[Tom Goddard]

Fixed.

I made mutationscores define clear all values for the specified attribute in all associated chains.

This bug was probably not noticed in the past because different attribute names were always used. But I changed the mutation structure coloring panel so it always uses the same attribute name "mutation_scores" unless the user renames the coloring to keep a record of it. The old scheme where all attributes got automatic names made the names useless because too many of them accumulated so it was hard to find the one you wanted.