PyMOL is a modeling visualization program for proteins.
Shortcuts
Color a protein by b-factor (or pLDDT)
spectrum b, minimum=0, maximum=100, selection=obj01
Color viridis-like
spectrum count, gold yellow green cyan slate violet
Change chain ID
select target_chain, object protein and chain B
alter target_chain, chain = 'Z'
sort
Morph PDBs
# requires that PDBs be aligned
morph morph_out1, model1, model2
morph morph_out2, model2, model3
# to combine multiple morphs
join_states combined_morph, morph_out1
join_states combined_morph, morph_out2