On Mon, May 2, 2011 at 2:18 PM, James M Holton <jmhol...@lbl.gov> 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? > Yes it makes sense that the weighting function for the integration would look like a spherical (or ellipsoidal) gaussian with a variance equal to the sum of the atomic MSD and form factor. > > 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. > The tricky part here is that I'd like to do this for density that is poorly-modeled by a single atom. An appropriate model might be a sum over ~10 different atomic positions each with its own B-factor and occupancy, but good luck getting someone to believe you. Since all I'm really interested in is "how much stuff" is there, I don't need to actually convince anyone that my occupancy/B-factor refinement is justified. F000 is going to make this whole thing suspect anyway. What I really want is an END map. Have you got code somewhere? I wasn't planning on sleeping tonight anyway... > > -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 >
