For scenarios like this, I often fall back to a little tinkering in the shell. First select the set of residues you want to view using the command line, then in the Python console:

from chimerax.atomic import selected_residues, concise_residue_spec

from chimerax.core.commands import run

residues = iter(selected_residues(session))

run(session, f'view {concise_residue_spec([next(residues)]}')

... and then just repeat the last line to view the next residue in your original selection until you run out.

On Thu, Apr 3, 2025 at 9:30 AM Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi Guillaume,

You can use:

info residue #1&ligand

This returns a list of all ligands in the log:

residue id #1/A:3000 name IHP
residue id #1/C:1500 name GTP

You can then do

view #1/A:3000

to focus the scene on that ligand.

Hope that helps,

Best, Matthias

From: Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu>
Date: Thursday, April 3, 2025 at 10:06
To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>
Subject: [chimerax-users] How to browse inspect ligands?

Hello ChimeraX team,

These days I look a lot a structures of photosystems, which contain large numbers of ligands: chlorophylls, carotenoids, etc. each by the dozens, adding up easily to more than 100 ligands.

Is there any tool to browse through all ligands systematically? Ideally something similar to the sequence viewer, but for ligands. Or a way to generate a list with chain IDs and "residue" numbers reported, and clicking rows in the list would select the corresponding ligand.

I looked for something like this, but couldn't find anything.

Thank you in advance,

Guillaume

När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/

E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

_______________________________________________
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu
To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu
Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

Altos Labs UK Limited | England | Company reg 13484917

Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT

VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert.
CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe.