[PyMOL] Structure align by sequence

Hi, 

I have a really just awful way of doing this and was wondering if there is a pymol solution that would make it easier.

Here is the problem.

Given two protein sequences, align their corresponding amino acids. The position of each of the strings is not known, just the sequence.

Ex.

Protein 1 - XXXXXXXXXXXXXXYYDFGHSFGXXXXXXXXXXX

Protein 2 - - XXXXXXYYDFGHSFGXXXXXXXXXXX


What I would like is to select the sequences (pseudocode obviously).

	select align_1 ,protein_1 and YYDFGHSFG
	select align_2, protein_2 and YYDFGHSFG
	align align_1, align_2
	RMSD is X.XX

Does this functionality exist?

Jordan

(apologize if you receive this in duplicate)