I read the rosetta tutorial for working with densities, available here:
In scenario 0, under the title "Density scoring terms in Rosetta" it is written that "Rosetta assesses agreement to density by computing the density that one would expect to see, given a model, and measuring the agreement of the expected and experimental density.".
The expected density is computing from the atom positions only right ? Since I am interested in converting an alphafold predicted model into a density map, I would like to get this expected density. How can I do that ?
In addition, what is tthe algorithm that computes this expected density ?
> converting an alphafold predicted model into a density map
Taking one step back do you have any empirical data —an MTZ file (reciprocal space)? And have you used Coot or Gemmi before jumping to Rosetta for your molecular refinement? If you have, do remember that the B factors are high=good which throws Phenix off as it expects high=bad.
If not, then density map is not the way. Constrains by pLDDT are the way forward. I actually wrote a note about it but for PyRosetta for vanilla Rosetta it would require some effort though to do.