I have tried both way and end up with different problem.
1) By editing the non-loop regions in loop templates. The resulted model contains a very strange loop region (the orientation of loop, which bends very high and leads to RMSD >5 for loop region backbone alone). So I tried to fix this problem by increasing the flanking conserved regions of the loops.But still I am getting the same problem.
2) By listing the sequence in aligment file as per usual Here I couldnot make the alingment for all four templates. Since the sequence length for one template is ~110 amino acids.
If I use the 2nd way by using the templates one by one keeping the each resulted model as myinitial model for modelling the next loop, Will it be a correct model ?
Please give me your valuable suggestions...
Selva
"" <> wrote:
I want to model an antibody structure with multiple templates for specific segments from each template based on the below alignment for two chains seperately. Since I know the domain interface residues, I could able to superimpose their relative orientation after modelling seperately.