I would suggest to play around with the alignment: misalign loop segments that you do not want to consider and use only the loop segment that you like, repeteadly.(see below). In fact you need at least a residue overlap on each side of the loops for proper orientation, unlike the simplified example shows below.

Andras

>P1;GoodL structureX;full.pdb:9::13::::: -------------------BBBB------------------------------* >P1;GoodL structureX;full.pdb:9::13::::: -----------------------------------BBBB--------------* >P1;GoodL structureX;full.pdb:1::45::::: AAAAAAAABBBBAAAAAAA----bbbbAAAAAAAA----bbbbAAAAAAAAAA* >P1;target sequence:target:::::::: CCCCCCCCCCCCCCCCCCCCCCC----CCCCCCCCCCCC----CCCCCCCCCC*

Troy Wymore wrote:

> Hello Modellers, > > I would like to restrain a loop that is repeated throughout my TARGET to > have the same conformation as the first loop conformation where the > alignment to the TEMPLATE is good. What is the easiest way to go about > this? DEFINE_SYMMETRY? > > Any help would be much appreciated, > > Troy Wymore > Biomedical Initiative Group > Pittsburgh Supercomputing Center