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<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
