I am trying to do modelling of a protein, for whom i got the hits for
psi-blast. Now, BLAST showed that the first ~100 residues to be in
homology with one set of proteins, and the rest with other set of
proteins. So for having the desired result, i broke the protein in two
parts, one part of first ~100 residues with two or more proteins showed
by BLAST search, and then the other part with its respectives subjects.
So now i have two modelled parts of protein, but dont know how to link
them, and important thing is that end of the former is the beginning of
the other. My questions are:
1. Is it the right way of doing?
2. If yes, can somebody suggest me how to link these parts?
3. An alternative way seems to be like alignment of chimeric protein,
but i am not able to get the desired results in first step of alignment
of the multiple templates. Can there be any way to give your own
alignment files as .ali and .pap? Because when i am trying to give
manually in the usual manner, then the program is looking for the
_fit.pdbs files formed at the first step, and complaining of no match...
I have really got stuck at the end.... :-( if anybody can please help me
out...........