On Mon, May 2, 2011 at 12:53 PM, Pavel Afonine <[email protected]> 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
>> density surrounding individual atoms for their calculations. Is there any
>> way to get that info out of either of them?
>>
>
> do you want to get electron density maps used in calculation of map CC? If
> so, then phenix.maps can compute any map defined as [p][m]Fo+[q][D]Fc, where
> p and q are any user-defined numbers. For example: 2Fo-Fc, 2mFo-DFc,
> 3Fo-2Fc, Fo-Fc, mFo-DFc, Fc, Fo etc...
>
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).
>
>
> Are the per-residue "Fo" and "Fc" columns in the output of
>> phenix.real_space_correlation actually what I am looking for?
>
>
> I'm not sure what you mean... Could you please explain? If you want to get
> electron density value (in sigma or e/A**3) computed at each atomic center
> (or any specified point in space), then phenix.map_value_at_point would do
> it.
>
Well the output of phenix.real_space_correlation has 'Fc' and 'Fo' columns
like so:
i_seq : PDB_string element occ b CC Fc Fo No.Points
FLAG
0 : " N SER C1002 " N 1.00 28.79 0.9871 2.58 2.75 52
1 : " CA SER C1002 " C 1.00 29.56 0.9945 2.67 2.58 58
2 : " C SER C1002 " C 1.00 31.68 0.9966 3.28 3.22 56
3 : " O SER C1002 " O 1.00 28.79 0.9971 3.51 3.55 55
4 : " CB SER C1002 " C 1.00 36.38 0.9531 2.06 1.80 56
Does the 'Fc' column mean that 2.58 is the average density in atom number 0
(based on F_calc)? If so is this in sigma? or e/A**3? Is this the average
density in some sphere surrounding the atom (like SFALL/OVERLAPMAP)?
Perhaps these are exactly the numbers that I would obtain from
phenix.map_value_at_point, in which case I've already got what I want.
>
>
>
>> If so what are the units and how is F000 handled?
>>
>
> It is not included.
>
> Pavel.
>
>
