To change chain ID, for example from chain A to chain B for the selection "junk":
alter (chain A) and junk, chain='B'
To change secondary structure, and manually assign them, alter can be used as follows:
alter 96-103/, ss='S'
alter 96-103/, ss='H'
alter 96-103/, ss='L'
And then, to see the effect type:
Fragment 183-189 highlighted in red:
alter 183-189/, ss='S'
I did it on purpose to show a dramatic (and non-sense) change. It is questionable whether and how to use this command, of course not to change an helix into a sheet!