Hi Pranav, You can select chains via their “description” attribute. In your case, this would be col #1&//description='Outer capsid protein VP4' red It also accepts regular expressions, so you could do col #1&//description='*VP4' red I really like the feature but am a lazy typer, so I saved some aliases that shorten the selection command to: des VP4 If you are interested how to do that, keep reading . 1. I saved a script called select_by_description.cxc, which only contains one line, namely: select //description='*$1*' 1. I then added an alias to run the script to the ChimeraX startup commands: alias des runscript /path/to/select_by_description_match.cxc $1 Now I can select the chain by simply typing des VP4. So the coloring command would become: des VP4 col sel red Note: This would affect all models, but you could change the select_by_description.cxc script to select #$1 &//description='*$2*' and the alias to alias des runscript /path/to/select_by_description_match.cxc $1 $2 and you could then match only the chains in model #1 with des 1 VP4 HTH, Matthias From: Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Date: Tuesday, September 30, 2025 at 11:50 To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Defining pdb chain ontologies Hi Team, I am writing to inquire about the functionality of ChimeraX, specifically concerning multi-subunit complexes with multiple chains of a single protein (e.g., PDB 4v7q). I am wondering if there is a feature that allows for manipulating chains by assigning them to functional ontologies. For instance, with the 4v7q example, I would like to be able to execute commands such as: color #1 "vp4" red `mm #1/"vp4" to #2/"vp4" These ontologies could be grabbed from the cif file and if the user decides define their pwn ontologies/groupings. If such a feature does not exist, would you consider exposing such a feature to the user? Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK