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