"color bynucleotide" changes unrelated colors

[Elaine Meng]

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.92 (2020-03-03)
Description
"color bynucleotide" changes coloring of protein surface

This is a problem with both the command directly and the "coloring" icon in the Nucleotides tab of the Toolbar.  Example:

open 3q5s
surface protein
color bynucleotide


Log:
> version

UCSF ChimeraX version: 0.92 (2020-03-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open 3q5s format mmCIF fromDatabase pdb

3q5s title:  
Crystal structure of BmrR bound to Acetylcholine [more info...]  
  
Chain information for 3q5s #1  
---  
Chain | Description  
A | Multidrug-efflux transporter 1 regulator  
B | 23 bp promoter DNA  
  
Non-standard residues in 3q5s #1  
---  
ACH — acetylcholine  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
  
3q5s mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
  

> surface protein

> color bynucleotide




OpenGL version: 4.1 INTEL-12.10.16
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.

[Greg Couch]

This an issue with the surface color method changing to be by atom. Only the color of the nucleotides was changed. But the surface of all of the atoms specified were colored. Will limit the atoms in the surface that are colored when bynucleotide is given just like what is done when byhetero is given. Are there any other cases that need to be fixed?

[Greg Couch]

Fixed.

[Elaine Meng]

Shouldn't "color bynucleotide" automatically restrict coloring to the "nucleic" specifier?  Target would still include atoms, ribbons, surfaces, labels... unless explicitly restricted by the user, but only for nucleic acid residues.   If not, could add an "& nucleic" to the command issued by clicking the icon, but right now I can't think of a downside to automatically restricting it.