Dear Pavel, I came across an example of calculating "electron_sums_around_atom" in cctbx <https://github.com/cctbx/cctbx_project/blob/master/cctbx/examples/fft_map_electron_density_around_atom.py>. 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 PDB-EDA <https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0236894> 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 <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 < > 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: lv...@posteo.de >> homepage: >> 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 >> >> 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/ >> > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > 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 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/
