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 an atom, or/and 2) you want
an array of points corresponding to the density values inside of a sphere
surrounding an atom of radius R (define R then - that's will be my next
question)?
> 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
>
Ok, sound like you asked it to calculate the map CC given two maps, {Fc,
Phc} and {Fo, Phc}. The values reported in the above columns are the
eight-point interpolated density values of corresponding maps computed at
atomic centers of listed atoms.
> Does the 'Fc' column mean that 2.58 is the average density in atom number
> 0 (based on F_calc)?
>
No, it is the eight-point interpolated density value of Fc map computed at
atomic center of atom number 0.
> If so is this in sigma?
>
Yes.
> or e/A**3?
>
No, but that's an option to request.
> Is this the average density in some sphere surrounding the atom
>
No, see above.
> (like SFALL/OVERLAPMAP)?
>
Hm.. I don't know , I've never used these programs. -:(
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.
>
I guess, we can get the numbers you want if we spend a few more iterations
of communicating (may be off-list at this point).
All the best!
Pavel.
