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
