rathankar rao wrote: > Iam in to modelling assignment of a zinc finger protein, which has > nearly 6 zinc fingers > The nearest template (1MEY) to it covers only 50% of the sequence length > and has 3 fingers corresponding to 3 chains in the template. > 1. i would like to know the method of representing the alignment in .ali > file for chain breaks
Use the / character to represent a chain break in your alignment. See http://salilab.org/modeller/manual/node175.html
> 2. i modelled this in a different manner. I aligned the query with the > template for only 50% of the sequence and assumed that these chains > belong to different pdb files and hence modelled the query protein like > what we do for a chimeric protein(without DNA chains). > *Outcome: *i got a 3D Model which did not represent the actual template, > since the coordinates of DNA was not incorporated in it. I dont know why > DNA was not built and as a result, the protein appeared to be bent.
To model DNA is like modeling any other non-standard ligand; see http://salilab.org/modeller/FAQ.html#10
Ben Webb, Modeller Caretaker