Viktor Hornak wrote: > I was trying to use Modeller to produce coordinates of parts of a given > target sequence based on full PDB coordinates of a template. > For example: my template has a sequence AAAAABBCCCCCDDEEEEE which > represents three helices (AAAAA, CCCCC, EEEEE) connected by two loops > (BB, DD). My target has a sequence aaaaabbcccccddeeeee (again three > helices and two loops) and I would like to overlap target helices on the > template helices such that the loops in target are ignored. In other > words, the resulting coordinates for the target would just have three > helices (aaaaa, ccccc, eeeee). I have tried different alignment > variants, such as: > > >P1;mol1 > structureX:mol1:1: :19: : :2.2: > AAAAABBCCCCCDDEEEEE* > > >P1;mol2 > sequence:mol2: : : : : : : > aaaaa--ccccc--eeeee* > > > but the target sequence always wants to be connected; I don't know how > to make Modeller to produce three helical fragments modeled on template > helices of the full PDB structure.

The sequence is connected because Modeller builds CHARMM stereochemical restraints on all atoms in a given chain, which include inter-residue backbone restraints. To get multiple fragments, just break the chain at the appropriate places by putting in chain break characters ('/'). So your alignment might look like

>P1;mol1 structureX:mol1:1: :19: : :2.2: AAAAABBCCCCCDDEEEEE*

>P1;mol2 sequence:mol2: : : : : : : aaaaa/-ccccc/-eeeee*

Ben Webb, Modeller Caretaker