Hi Matt,
I'm trying to 'measure' the density in a region of my structure by > integrating the electron density there (notwithstanding errors in F000). I > understand that both overlapmap and phenix.real_space_correlation compute > density surrounding individual atoms for their calculations. Is there any > way to get that info out of either of them? > do you want to get electron density maps used in calculation of map CC? If so, then phenix.maps can compute any map defined as [p][m]Fo+[q][D]Fc, where p and q are any user-defined numbers. For example: 2Fo-Fc, 2mFo-DFc, 3Fo-2Fc, Fo-Fc, mFo-DFc, Fc, Fo etc... Are the per-residue "Fo" and "Fc" columns in the output of > phenix.real_space_correlation actually what I am looking for? I'm not sure what you mean... Could you please explain? If you want to get electron density value (in sigma or e/A**3) computed at each atomic center (or any specified point in space), then phenix.map_value_at_point would do it. > If so what are the units and how is F000 handled? > It is not included. Pavel.
