This may be too late to be of use, but as one of the authors of the 
sfall/overlapmap system..

sfall does generate a coded map which flags every grid point with a 
unique ID of the nearest atom, ie one which is unique providing there 
are not too many atoms - it is adequate for most molecules though prob. 
not for the ribosome..
A grid point is assigned the ID of the nearest atom.
And the default radius of an atom is indeed 2.5A, which will generate 
overlap between most atoms.

However for a reasonable B factor and a fine grid (SFALL has a default 
grid spacing of 0.5A) most of the significant density is correctly 
assigned to a given atom. So the CC is reasonably accurate for atoms 
with acceptable B factors, but not very accurate for those with B> 100 say..

Eleanor


On 05/02/2011 07:18 PM, James M Holton wrote:
> 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<[log in to unmask]>  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