On Tue, Jun 24, 2014 at 1:11 AM, Egor Tchesnokov < etchesnokov@chemistry.otago.ac.nz> wrote:

Thank you for the comment. The model I use for Phaser is coming from Sculptor, so it does not have heteroatoms. I introduce heteroatom (Fe) only after Phaser. I use Phaser-EP to find it, eventhough it is obvious from the density. Then I merge Fe and Phaser.pdb in Coot after which I feed it to ReadySet. So the pdb that I give to Refine either have Fe with occupancy of 1, <1 or >1 (I tried both). I use PDB editor to add charge, but the outcome is still the same. After refinement Fe occupancy is either 1 or very close.

My apologies, I misinterpreted your message. Is this just a case of "name that blob?" If so, I suggest posting images of the density around the iron to the list (and probably ccp4bb as well) asking for suggestions. It's very likely that someone will have encountered similar density before. -Nat