Default color targeting issue

[Tristan Croll]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.7rc202311140124 (2023-11-14 01:24:52 UTC)
Description
This *feels* bug-like (albeit minor): if I use the command "color {element} {color}", then unless I remember to explicitly add "target a" to the end of the command, then the color is also applied to the ribbon for every residue with an atom of that element. I think it make sense for such commands to only apply to the atoms by default.

Log:
> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.7rc202311140124 (2023-11-14)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3io0

3io0 title:  
Crystal structure of EtuB from Clostridium kluyveri [more info...]  
  
Chain information for 3io0 #1  
---  
Chain | Description | UniProt  
A | EtuB protein | A5N734_CLOK5 75-304  
  
3io0 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> color H lightgrey

> show

> color H lightgrey

> addh

Summary of feedback from adding hydrogens to 3io0 #1  
---  
notes | Termini for 3io0 (#1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A PRO 76  
Chain-final residues that are actual C termini: /A PHE 304  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue /A PHE 304  
198 hydrogen bonds  
1692 hydrogens added  
  

> color H lightgrey

> color bychain

> color C lightgrey

> color bychain

> color O lightgrey

> color bychain

> color S lightgrey




OpenGL version: 3.3.0 NVIDIA 529.08
OpenGL renderer: NVIDIA GeForce RTX 3070 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_GB.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: HP
Model: HP ZBook Studio 15.6 inch G8 Mobile Workstation PC
OS: Microsoft Windows 11 Pro (Build 22621)
Memory: 34,007,068,672
MaxProcessMemory: 137,438,953,344
CPU: 16 11th Gen Intel(R) Core(TM) i7-11800H @ 2.30GHz
OSLanguage: en-GB

Installed Packages:
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[Tom Goddard]

That would be nice. But ChimeraX commands that take an atom specifier just get a list of atoms. The command does not know that it came from an element selector. In other words the color command Python code does not know whether the command was "color H white" or "color /B white". In either case it just gets a list of atoms.

In theory the selectors like H (element name), protein, helix, ... (these are defined in chimerax/atomic/selectors.py) could add an attribute to the Atoms instance that they produce like atoms.element_selector = True. But then what happens with "color C|H white"? Here the atom spec parsing is going to combine the two sets of atoms. How will it know about the "element_selector" attribute. What about "color H & protein white"?

The technical problems of changing command behaviors based on what the atom specifier looked like when it was typed seem too great. Even if the technical problems were handled in some way, the complexity added for a user to understand how a command works makes this not clearly an improvement. Magical command behaviors are nice when they work but can then waste hours of users time figuring out rare cases when they don't do the usual thing.

[Eric Pettersen]

I think the only realistic way to implement this is to not target ribbon color unless all the atoms of the residue are included. I'm guessing that would lead other unexpected behaviors.

[Tom Goddard]

The command the user needs is "color H white atoms". It is hard to imagine how they would figure that out without reading documentation. This makes coloring by element with this command not useful to most people since they won't read documentation. That is true of many of the feature of ChimeraX, they are of no use unless the user reads documentation.

[Tom Goddard]

Even the graphical user interface has this problem. Using menu Select / Chemistry / Element / H and menu Actions / Color / White will issue the command "color sel white" that colors the ribbon in addition to the atoms.

[Tristan Croll]

FWIW, the reason this came up is that when using soft or gentle lighting,
pure-white hydrogens become almost invisible on a white background. I find
that colouring them lightgrey works better.

On Wed, 6 Dec 2023 at 21:07, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>

[Eric Pettersen]

You have to use Actions→Color→All Options to get full control over the coloring in the GUI.

Not that this is relevant to Tristan's point, since he's using the command.