RFE: ligand browser

[guillaume.gaullier@…]

"If the ChimeraX team has enough capacity, I still think it would be a nice feature to have in a more easily discoverable form (i.e. with a GUI tool like the sequence viewer), because browsing ligands is a task even beginners could need to do when inspecting models."

While the ligand table in the log covers some of this, it's awkward when there's multiple copies of the same ligand in the structure to focus in on each in turn.

[guillaume.gaullier@…]

Thank you for opening this ticket!

I will add here some details about what I meant in the discussion on chimerax-users.


The idea of this feature is to enable easy inspection of every ligand and its local environment in a structure, assuming the number of ligands can be large (more than 100). Two things would greatly facilitate this task:


1. A "browsing" mode that centers the view on the next or previous ligand. It should only require a single click or key press. Or a single command that doesn't need a new parameter for the next ligand and can simply be repeated by pressing enter again (so not like "view :201", which needs to be edited to "view :202" and so on and so forth to keep browsing), like the residue stepper command in ISOLDE "isolde step next" / "isolde step prev".


2. A way to list every ligand present in the structure, with its 3-letter residue code, chain and residue number. This already exists, but gives a plain text output. Ideally, the tool would produce a table, and clicking a row would both select the corresponding ligand and center the view on it. An interface similar to the validation tools in ISOLDE would be ideal. Browsing the table with up/down arrow keys could be an alternative to the "browsing mode", if the table is easier to implement; so in this way, maybe these two features are really just one. Not sure what would make the most sense.


Thanks again, and I'm happy to discuss UI details if needed.

________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Thursday, April 3, 2025 7:53:57 PM
To: Guillaume Gaullier; pett@cgl.ucsf.edu
Cc: goddard@cgl.ucsf.edu; meng@cgl.ucsf.edu
Subject: [ChimeraX] #17281: RFE: ligand browser

#17281: RFE: ligand browser
--------------------------------------+-------------------------------
 Reporter:  guillaume.gaullier@…      |               Owner:  pett
     Type:  enhancement               |              Status:  assigned
 Priority:  moderate                  |           Milestone:
Component:  Surface/Binding Analysis  |             Version:
 Keywords:                            |          Blocked By:
 Blocking:                            |  Notify when closed:
 Platform:  all                       |             Project:  ChimeraX
--------------------------------------+-------------------------------
 "If the ChimeraX team has enough capacity, I still think it would be a
 nice feature to have in a more easily discoverable form (i.e. with a GUI
 tool like the sequence viewer), because browsing ligands is a task even
 beginners could need to do when inspecting models."

 While the ligand table in the log covers some of this, it's awkward when
 there's multiple copies of the same ligand in the structure to focus in on
 each in turn.
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/17281>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

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