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 <[email protected]> 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 > > > > ######################################################################## > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > -- > > =============================================================== > * * > * Gerard Bricogne [email protected] * > * * > * Global Phasing Ltd. * > * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * > * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * > * * > =============================================================== > -- Sen Yao, PhD Center for Environmental and Systems Biochemistry Markey Cancer Center University of Kentucky, Lexington KY ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
