elegant way to color pLDDT from JSON into CIF for visualization?

[mintuora]

Hi RF3 / AtomWorks team,

I have a question regarding visualization of pLDDT / confidence scores produced by RF3, and whether there is an official or recommended workflow for mapping them into CIF files for coloring.

When running RF3 inference, we obtain confidence information (e.g. pLDDT or related scores) in the generated JSON outputs. However, when inspecting the visualization utilities provided by AtomWorks, I noticed that:

from atomworks.io.utils.visualize import view
from atomworks.io import parse

the current view() implementation (based on py3Dmol) colors structures by chain / polymer type, but does not appear to support coloring by pLDDT or other confidence values.

In particular:
view() does not read pLDDT from JSON
there is no obvious helper to map per-residue confidence → per-atom values
CIF output does not seem to include pLDDT in B-factor (or an equivalent field) by default

Question
Is there an official or recommended approach in RF3 / AtomWorks to:
Take pLDDT (or confidence scores) from the RF3 JSON outputs
Map them onto the structure (e.g. residue → atom broadcasting)
Encode them into CIF (e.g. via B-factor or a custom mmCIF field)
Enable downstream visualization (PyMOL / py3Dmol / ChimeraX) with confidence-based coloring

Thanks a lot for your work on RF3 and AtomWorks — any guidance or pointers would be greatly appreciated!

Best regards