The CCP4 program that makes the "label map" you are looking for is SFALL. It can be told to make a .map file where each grid point is still a floating-point number, but instead of the usual electron density it "encodes" the residue number, atom number, etc. The OVERLAPMAP program knows how to decode this, and you specify it as a third map, in addition to the two you want to correlate.
However, the distance from the center of each atom that is still "part of it" is an interesting question. I think the default is 2.5 A or so, but this depends on the B factor, and probably grid points far from the center of an atom "should" count less than ones near the middle? If what you really want is the number of electrons in a region, then I would recommend occupancy refinement (which you can now do in REFMAC), and then adding up occ*Z for the atoms of interest (where Z is the atomic number). This has the nice property of being independent of F000 estimates. -James Holton MAD Scientist On May 2, 2011, at 11:44 AM, Matt Warkentin <mattw...@gmail.com> wrote: > Hi all > > 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? > > Are the per-residue "Fo" and "Fc" columns in the output of > phenix.real_space_correlation actually what I am looking for? If so what are > the units and how is F000 handled? > > Thanks a bunch to anyone who can clear this up. > > Matt
