Hi,

I have a single sequence and several structures of different conformations of the same protein. I would like to use this information to create a single alignment that incorporates the data from all the conformations. The structures are all of the same protein, so they have the same sequence. Once I have the single alignment, then I can use this alignment to create a model for each conformation. Also note that because of the different conformations, the alignment of the sequence with structure A is not (necessarily) the same alignment given if I align the sequence with structue B.

My main approach has been to append the structures and the sequence to alignment and then run align2d(). The problem I have here is that because all the structures have the same sequence, the returned alignment just has all the protein sequences aligned with no gaps and my single sequence is just added with all the extra residues overhanging(the sequence is a little longer that the protein sequences) the alignment of the proteins. Is there some way to add a weight to the protein sequences so that they don't overpower the single sequence? Since the protein sequences align perfectly, the addition of the single sequence is negligible to the overall alignent.

I thought this was what the align_what='BLOCK' argument was supposed to do, but I didn't have any luck with that either--I tried to put the proteins in one block, and the sequence in another. I've also been trying salign() without success.

I'm new to Modeller and this problem seems sufficiently different from the tutorials and examples in the manual to leave me at a loss. Would someone give me some guidance about how to approach this?

Thank you, Jim Fonseca