Assembly of discontinuous domains with continuous domains

All could be decomposed into the following three cases, supposing there are 1...n domains:

1. n=2, domain 2 is inserted in the middle of domain 1.

==> pmodel1.pdb=part 1 of domain 1, pmodel2.pdb=domain 2, pmodel3.pdb=part 2 of domain 1.

2. domains 1 to i, j to n have relative positions/orientations fixed, domains i+1 to j-1 have relative positions/orientations fixed.

==> pmodel1.pdb=domain 1 + ... + domain i, pmodel2.pdb=domain i+1 + ... + domain j-1, pmodel3.pdb=domain j + ... + domain n.

3. domains a to i, j to b have relative positions/orientations fixed, domains i+1 to j-1 have relative positions/orientations fixed. They are fexible to all the remaining domains.

==> pmodel1.pdb=domain a + ... + domain i, pmodel2.pdb=domain i+1 + ... + domain j-1, pmodel3.pdb=domain j + ... + domain b.

Treat the assembled result modela-b.pdb as a whole, which contains domains a to b, then conduct continuous domain assembly.

==> pmodel1.pdb=domain 1, ..., pmodela.pdb=modela-b.pdb, pmodela+1.pdb=domain b+1, ... pmodeln+a-b.pdb=domain n.