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