One of the most successful programs for generating protein models is called Modeller and it works on a rather different principle from that described above.
The first two stages are the same as before: identifying one or more parents and generating an alignment between the parents and the target sequence. However, rather than the conventional "spare parts" approach described above, a molecular dynamics approach is used to assemble the SCRs and SVRs in a single step.
A conventional molecular dynamics (MD) force-field is used and Newton's laws of motion are integrated in the conventional manner. However, additional restraints are imposed in the force-field, known as a "probability density function" (PDF). This is essentially a set of preferred inter-C-alpha distances calculated from the parent structure(s). Where more than one parent structure is used, the PDF is weighted such that regions which are highly conserved in structure have stronger restraints while regions which vary more in structure have weaker restraints.
Modeller does allow the user to explore local areas of the structure (generally SVRs) in more detail if desired.
Information on Modeller may be obtained from the author's web page (http://guitar.rockefeller.edu/ ) and it is described in the paper: Sali & Blundell, (1993) J. Mol. Biol. 234, 779-815