Dear Sen,

     Our messages just crossed ... .

     With best wishes,

          Gerard.
--
On Tue, Mar 05, 2019 at 11:32:01AM -0500, Yao, Sen wrote:
> Dear Gerard,
>
> Thank you for your reply. I totally agree with you.
>
> The average value of the 2mFo-DFc map should be zero, and from my
> observation, most of them are a very small number (<0.001) that can be
> viewed as zero practically. As Pavel mentioned, phenix.f000 will give you
> F(0,0,0) value, but I don't see that information stored and easily
> calculated from .ccp4 data.
>
> Your solution to add up the electrons in the model and divide by the number
> of voxels related to the model is in essence what I did to aggregate the
> atoms into chains. The problem is determining the voxels to include which
> require the radii determined for each atoms. For that I optimized the radii
> for each atom type using the criteria that all atoms need to include a
> significant number of electrons and give a consistent result across the
> whole PDB structures.
>
> And with all that, I got this ~1/3 value of the theoretical number of
> electrons. I guess what I have to do is to use this ratio and convert them
> back to an actual number of electron meaning.
>
> Thank you all for the input!
>
> Cheers,
> Sen
>
>
> On Mon, Mar 4, 2019 at 1:21 PM Gerard Bricogne <[log in to unmask]>
> wrote:
>
> > 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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>
> --
>
> Sen Yao, PhD
> Center for Environmental and Systems Biochemistry
> Markey Cancer Center
> University of Kentucky, Lexington KY