Dear All, 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...........
Thanks in advance... Monika