Dear Sen,
I may be unaware of special features of these maps, but if they
are computed in conventional ways, they lack an F000 term. Therefore
the average value of the 2mFo-DFc map is zero, just as if it was a
difference map. This may explain why you do not find all the electrons
you would be expecting. To get this right, you would need to add that
F000 term to the set of Fourier coefficients going into the
calculation of the map. You can get a pretty satisfactory F000 value
by taking it from the Fourier transform of the model density, and
applying the appropriate scale factor. Unfortunately not all structure
factor programs will give you that F000. Instead, then, you can add
the numbers of electrons for all the atoms of your model in the unit
cell, put it on "map scale", divide it by the number of voxels in that
unit cell, and add it to all the map values in all the voxels you
examine.
In any case, the use of a zero-mean map would be the cause of
your 1/3 factor.
Apologies to the PDBe if they have already thought of that and
are including the F000 (or average number of electrons per voxel) into
the calculation of their maps - I didn't see any sign that this was
being done.
With best wishes,
Gerard.
--
On Mon, Mar 04, 2019 at 10:36:11AM -0500, Yao, Sen wrote:
> Hi all,
>
> I have been using the electron density maps available on the PDBe website
> to run some analysis. And I run into this question that I hope that I can
> get some help from the community.
>
> In the ccp4 format, the electron density is represented as a 3-d array map,
> with each number corresponds to the density value of a voxel in real space.
> If I add all voxel densities around an atom together and divided it by the
> number of electrons of that atom, in theory it should give me a ratio with
> the unit Å-3 (angstrom to the power of -3), and this ratio should be
> inversely related to the voxel volume. (Correct me if I am wrong here.)
> However, after I got this ratio for each atom, aggregated it into chains
> and calculated a median, and then compared the chain median to the voxel
> volume over all PDB structures with electron density available, they show a
> slope of ~1/3 instead of expected 1 (see attached link). That is, almost
> all the values in the electron density maps are only about 1/3 of
> represented electrons.
>
> https://drive.google.com/file/d/1K_3uxZfUPuTdH1DtKJgKHLRUA5NHTVPB/view?usp=sharing
>
>
> So my question is, is there a conversion or scaling factor that PDBe uses
> to generate the ccp4 files? If so, is that information stored in the ccp4
> files or anywhere else? And if not, why do I observe this 1/3 ratio pretty
> consistently across the whole PDB?
>
> I would really appreciate any insights on this matter. Thank you!
>
> Sincerely,
> Sen
>
> --
>
> Sen Yao, PhD
> Center for Environmental and Systems Biochemistry
> Markey Cancer Center
> University of Kentucky, Lexington KY
>
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--
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