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To align two pdb, prot1 and prot2

align prot1////ca, prot2////ca

It may be necessary to restrict the alignment region to certain chains.
For example, to match chain A to chain B:

align prot1//A//ca, prot2//B//ca


align prot1 & i. 90-100 & n. ca, prot2 & i. 90-100 & n. ca

will align prot1 and prot2 just on the segment shown (90-100).
To avoid refinement of the alignment add 0,0 at the end:

align 1kjg & i. 1-99 & n. ca, 1kjh & i. 1-99 & n. ca, 0, 0


pair_fit prot1///1-99/ca, prot2///1-99/ca

pair_fit will use all atoms, whereas align will only use atoms that are matched with respect to a dynamic-programming sequence alignment. Disadvantage of pair_fit is that the atoms number must be equal.