Also check if the mean value of the map over the ASU is zero. If so, the map was probably calculated without the 0,0,0 term of the Fourier series, so zero does not represent zero density but rather the mean density.
On 03/04/2019 12:43 PM, Ian Tickle wrote:
Hi Sen If you multiply the electron density in a voxel by the voxel volume you should get an estimate of the number of electrons contained in that voxel, and then you can add up the numbers of electrons in all the voxels occupied by an atom to get the total number of electrons in that atom, which is basically the same as what you are saying. However note that the electron density is a point sample: it's not the average density in the voxel, so the above calculation won't be quite accurate, depending on the 'smoothness' of the density. This is like the error in an integral by use of Simpson's rule. To be sure of accounting for all the density you need to sample it finely, say not more that Dmin/4. There are two more issues here: first the atomic positions are never error-free which reduces the contribution to the density by the factor D in the expression 2mFo-DFc (or mFo for centric phases) for the map coefficients. So if the errors were sufficiently large D would tend to zero and you would get no density at all! The density that you see is really only that part of the true density for which there is evidence in the experimental data. Second, what exactly do you mean by "add all voxel densities around an atom"? The electron density could easily extend 2 Ang. from an atomic centre, depending on the atom's finite size (represented by the form factor), its thermal motion (B factor) and series termination effects (resolution). So if you don't go out far enough you will fail to account for some fraction of the electron count. The problem is of course you can't go so far as to overlap bonded atoms which will be well within 2 Ang. distance. The standard method of dealing with this is to represent 'soft' atoms (where the distance between atoms may be less than the sum of their radii) as Voronoi polyhedra (like the packing of soap bubbles!). Is that how you handled it? Cheers -- Ian On Mon, 4 Mar 2019 at 15:47, Yao, Sen <[email protected] <mailto:[email protected]>> 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 <https://urldefense.proofpoint.com/v2/url?u=https-3A__drive.google.com_file_d_1K-5F3uxZfUPuTdH1DtKJgKHLRUA5NHTVPB_view-3Fusp-3Dsharing&d=DwMFaQ&c=ogn2iPkgF7TkVSicOVBfKg&r=cFgyH4s-peZ6Pfyh0zB379rxK2XG5oHu7VblrALfYPA&m=DQk9GIsPtYWv1IJTpGpK8ZW9vGk3XjlPB0GbBPxwYjo&s=z5pf9EEAoR1DrakQMp9nTAQ-Z4Sp5tigP5O4-Phm4WU&e=> 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 <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=ogn2iPkgF7TkVSicOVBfKg&r=cFgyH4s-peZ6Pfyh0zB379rxK2XG5oHu7VblrALfYPA&m=DQk9GIsPtYWv1IJTpGpK8ZW9vGk3XjlPB0GbBPxwYjo&s=VYiyWIusOXosLHKGq4Rnre-WXsRQLNHA90afdyNvizo&e=> ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=ogn2iPkgF7TkVSicOVBfKg&r=cFgyH4s-peZ6Pfyh0zB379rxK2XG5oHu7VblrALfYPA&m=DQk9GIsPtYWv1IJTpGpK8ZW9vGk3XjlPB0GbBPxwYjo&s=VYiyWIusOXosLHKGq4Rnre-WXsRQLNHA90afdyNvizo&e=>
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