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 tho
Hi Matt,
What I want is the density 'inside' each atom in the map, so that I can make
> quantitative comparisons of "how much stuff" is present in a blob (modeled
> or not).
>
that's still ambiguous...: 1) do you want a density value calculated at a
point, which may be, for example, a center for
On Mon, May 2, 2011 at 2:18 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 num
On Mon, May 2, 2011 at 12:53 PM, Pavel Afonine wrote:
> 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
>>
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 de
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
