[phenixbb] Question about occupancy and 2Fo-Fc and Fo-Fc maps

Vatsal Purohit vpurohi at purdue.edu
Tue May 3 13:55:11 PDT 2022

Hi everyone,

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?
  2.  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?

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


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