On Fri, 28 Dec 2007 15:55:39 +0000
Brenda Patterson <[EMAIL PROTECTED]> wrote:
Hello,
I am fairly new to this lark
No problem. With a name like Patterson, your future is guaranteed (unless of
course you see everything in the world with intensity but no phase).
I have a density in my difference map which resembles my ligand. The
thing is,
it overlaps the density map of my structure and if I were to place the
ligand
in that map, then there would be a steric clash. ... how
to proceed?
The best thing to do at this point is to refine your structure while omitting
the residues involved in the potential steric clash. The ligand may bind by
induced fit -- i.e., changing the conformation at the binding site from that of
the original structure. When you do that, the density that comes back will be
less biased, and the answer to how it fits together may be apparent at that
point.
