“alter” is a useful function in PyMOL. One can use “alter” to renumber residues, rename chain IDs, re-define secondary structures et al. More details can be found at PyMOLWiki.

Here I am showing a simple example that using “alter” to redraw secondary structure of ubiquitin (PDB: 1UBQ).

Example commands: (two steps, alter object, then run "rebuild")
alter 40-45/, ss='L' 
rebuild
(see second image.  the beta strand is shown as loop, cartoon mode)
alter 40-45/, ss='H' 
rebuild
(see third image, the beta strand is shown as helix, cartoon mode)

More example commands of alter:
(A), alter chainID
alter (chain A),chain='B' 
sort
(B), alter residue numbers of chain A
alter (chain A),resi=str(int(resi)+1000) 
sort