Dear Sriram, dear Jon, The sum of values of a map (always calculated at some finite resolution) is not the same as a sum of density values. In such maps, a contribution of each atom is a function oscillating with the distance to the atomic center. Even when the height of these ripples is relatively small, surprisingly, the sum (integral) of the map values converges very-very slowly (not like for a density itself!) with the radius at which you truncate you sum. See for example §3.2 and Figs. 3-4 in a our recent article in Acta Cryst D (2022), D78, 1451-1468.
So one should be very careful with interpretations of such formally calculated sums (again, even when you have F000, absolute scale etc). With best wishes, Sacha Urzhumtsev ----- Le 29 Juin 23, à 3:10, sriram raghavan <hypowergrav...@gmail.com> a écrit : > Dear Pavel, > I came across an example of calculating "electron_sums_around_atom" in [ > https://github.com/cctbx/cctbx_project/blob/master/cctbx/examples/fft_map_electron_density_around_atom.py > | cctbx ] . If we don't zero the F000 or if we normalize the density of the > real-space map by the unit cell volume and the scattering factor of the unit > cell (F000), we can obtain the value of the density and sum the values of the > positions of the obtained grid points on the map. This approach will yield the > electron density sum across the volume, correct? > Additionally, there is a tool called [ > https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0236894 | > PDB-EDA ] that performs a similar calculation but not on selected volume. > Best regards, > S. Sriram > On Thu, Jun 29, 2023 at 4:03 AM Pavel Afonine < [ mailto:pafon...@gmail.com | > pafon...@gmail.com ] > wrote: >> Hi Jon, >> not really the answer to your question but.. This may be very tricky to do >> because what you look at is not an electron density map but its Fourier image >> of finite resolution phased by crystal model (that has errors), plus >> experimental errors, and missing F000 (which is not measured as part of your >> diffraction experiment). So.. if such a software exists I'd be very cautious >> interpreting the results you get from it! >> Pavel >> On Wed, Jun 28, 2023 at 9:16 AM Hughes, Jonathan < [ >> mailto:jon.hug...@bot3.bio.uni-giessen.de | >> jon.hug...@bot3.bio.uni-giessen.de >> ] > wrote: >>> hello everyone, >>> is there software that can use an electron density map to quantify the >>> number of >>> electrons in a selected volume somewhere in a protein? >>> cheers >>> jon >>> -- >>> Professor Jon Hughes, BSc, PhD >>> Department of Physics >>> Free University of Berlin >>> Arnimallee 14 >>> 14195 Berlin >>> Germany >>> mobile: (+49/0)1757929098 >>> email: [ mailto:lv...@posteo.de | lv...@posteo.de ] >>> homepage: >>> [ http://www.uni-giessen.de/fbz/fb08/Inst/pflphys | >>> http://www.uni-giessen.de/fbz/fb08/Inst/pflphys ] >>> Sent without the use of Apple products >>> ######################################################################## >>> To unsubscribe from the CCP4BB list, click the following link: >>> [ https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 | >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ] >>> This message was issued to members of [ http://www.jiscmail.ac.uk/CCP4BB | >>> www.jiscmail.ac.uk/CCP4BB ] , a mailing list hosted by [ >>> http://www.jiscmail.ac.uk/ | www.jiscmail.ac.uk ] , terms & conditions are >>> available at [ https://www.jiscmail.ac.uk/policyandsecurity/ | >>> https://www.jiscmail.ac.uk/policyandsecurity/ ] >> To unsubscribe from the CCP4BB list, click the following link: >> [ https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 | >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ] > -- > With Regards > S.Sriram > To unsubscribe from the CCP4BB list, click the following link: > [ https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 | > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ] ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
