Editing Modeling and Editing Structures (section)

==Superposition of two molecules==
Using pair_fit requires that you specify a set of paired atoms in each structure. Fortunately, you no longer have to specify each pair separately, so long as the ordering is the same in each selection (almost always true).
<source lang="python">
pair_fit ( trna10 and resid 10:15 and name P ), ( ref4 and resid 10:15 and name P )
</source>

Another example:
<source lang="python">
pair_fit prot1///11-26/CA, prot2///34-49/CA
</source>
would superimpose prot1 on prot2 using C-alphas from residues 11-26 in prot1 and 34-49 in prot2.