On 28/12/2007, Brenda Patterson < [log in to unmask]> wrote:

Hello,

I am fairly new to this lark so please forgive me if this question is unclear,
but it is really puzzling me.

I have used phaser to generate a molecular replacement structure of my target
(which has 100% identity to my template) and this particular crystal I had
soaked with a ligand.

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.  Obviously I would expect the
ligand to be near to the structure, but not overlapping it?  I am
uncertain how
to proceed?

Any helpful suggestions please?

Thanks in advance

Brenda