Hi Vatsal,

I had 2 questions regarding occupancy and maps generated in ligand-bound regions for various ligand models potentially present in the structure:

1. I’ve been working with some 2.0 angstrom structures and trying out refinements with 2 sets of bound ligands at varying occupancies (at the same active site) to get an approximate idea of their relative populations in the structure. For one set of ligands, I observe 2Fo-Fc density in regions uniquely occupied by them even when their occupancy is zero. Could there be a reason why this is the case?

how you know that their occupancy is zero? Did you try to refine occupancy starting with some non-zero value and it refined to zero? If the ligand is there and it is not present in your model and you can see some evidence of it in Fo-Fc and 2Fo-Fc maps, then the ligand is needed there! Or could it be the occupancy refinement wasn't set up well and resulted in zero value?

1. Additionally, I observe red Fo-Fc density in the same region when the occupancy is set to 1.0. It disappears at lower occupancies of 0.7 indicating that a lower population of this ligand is present. However, when the occupancy is very low, we don’t see an equivalent green Fo-Fc density popping up in the same region. Could there be a reason for why the red Fo-Fc density at high occupancy doesn’t translate to green Fo-Fc for the same region at low occupancy?

Negative Fo-Fc map in the presence of fully occupied ligand in the model obviously means there is more scaterring in the model than needed. It is unsurprising that negative density disappears when you lower the occupancy. All this tells me only one thing: you need to *refine* occupancy.

Any information or resources that could give me more insight into this question would be really helpful!

This is relevant to your questions: https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN... Pavel