That's super neat! (albeit a bit convoluted :)). I wonder if it is possible to create custom descriptions, say at the start of a session, I am particularly thinking about the case where the model is being iteratively built and refined and perhaps at that stage these descriptions are not registered in the cif (and def not in PDB) files. 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 On Tue, Sep 30, 2025 at 12:49 PM Vorländer,Matthias Kopano <matthias.vorlaender@imp.ac.at> wrote:

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 .

I saved a script called select_by_description.cxc, which only contains one line, namely:

select //description='*$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

Thanks Elaine! This might just do! :) 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 On Tue, Sep 30, 2025 at 6:49 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Pranav, You can arbitrarily name any atom specification with the "name" command. See:

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/name.html>

Example commands:

open 4v7q name vp4 /bx /by /bz color vp4 red

You may or may not want the "frozen" option of the name command, see the help link above.

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Sep 30, 2025, at 10:06 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

That's super neat! (albeit a bit convoluted :)). I wonder if it is possible to create custom descriptions, say at the start of a session, I am particularly thinking about the case where the model is being iteratively built and refined and perhaps at that stage these descriptions are not registered in the cif (and def not in PDB) files. 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

On Tue, Sep 30, 2025 at 12:49 PM Vorländer,Matthias Kopano <matthias.vorlaender@imp.ac.at> wrote:

...

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 .

I saved a script called select_by_description.cxc, which only contains one line, namely:

select //description='*$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

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