Modify Visualization in VMD

Once your PDB file is loaded in VMD, you can change the visual style using the Graphical Representations menu.

Representation settings

Drawing Method: Set to NewCartoon to show ribbon structure.

Coloring Method: Set to Beta to visualize pLDDT confidence values (stored in the beta column).

Result

Resulting visualization colored by pLDDT via ‘beta’ slot.
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