Hi, pointers listed here may be of help: 1) CCP4 Newsletterhttp://www.ccp4.ac.uk/newsletters/newsletter42/content.html On the Fourier series truncation peaks at subatomic resolution Anne Bochow, Alexandre Urzhumtsev
2) https://www.phenix-online.org/presentations/latest/pavel_maps.pdf 3) Central Ligand in the FeMo-Cofactor Nitrogenase MoFe-Protein at 1.16 Å Resolution: A. Oliver Einsle, et al. Science, 1696 (2002) 297 4) Page 267 Figure 4: On the possibility of the observation of valence electron density for individual bonds in proteins in conventional difference maps P. V. Afonine, V. Y. Lunin, N. Muzet and A. Urzhumtsev Acta Cryst. (2004). D60, 260-274 Pavel On Thu, Sep 13, 2012 at 2:09 PM, Niu Tou <niutou2...@gmail.com> wrote: > Dear Colleagues, > > I am trying to repeat a series termination effect calculation displayed as > figure 2 in a publihsed paper (http://www.ncbi.nlm.nih.gov/pubmed/12215645). > Formula > (1) was used to implement this calculation. Since f(s) is not defined in > detail in this paper, I used formula and parameters listed in another > paper (http://scripts.iucr.org/cgi-bin/paper?a05896) to calculate it. > > However, the result I got is not consistent with figure 2 of the first > paper. I am not sure if the formulas I used are right or not. Or if there > is any problem in the MatLab code, which I list below: > > ########### > > clear all;clc;format compact;format long; > > > > % matrix of a, b, c coefficients: > > % rows: Fe, S, Fe1, Mo > > % columns: A1; B1; A2; B2; A3; B3; A4; B4; C > > fM = ... > > [11.9185 4.87394 7.04848 0.34023 3.34326 15.9330 2.27228 79.0339 > 1.40818;... > > 7.18742 1.43280 5.88671 0.02865 5.15858 22.1101 1.64403 55.4651 > -3.87732;... > > 11.9185 4.87394 7.04848 0.34023 3.34326 15.9330 2.27228 79.0339 > 1.40818;... > > 19.3885 0.97877 11.8308 10.0885 3.75919 31.9738 1.46772 117.932 5.55047]; > > > > %%% store radius data: > > % distance from: origin > > % columns: Fe, S, Fe, Mo > > R_el = [2.0 3.3 3.5 3.5]; > > RHO_t = zeros(4,400); > > for numel = 1:4 > > EL = numel; > > RHO = zeros(1,400); > > dmax = zeros(1,400); > > for iter = 1:400 > > dmax(iter) = iter/100; % in angstroms > > % numerical integration > > int_fun = @(s) 4*pi*(s.^2).* ... > > (fM(EL,1).*exp(-fM(EL,2).*(s.^2)*0.25) + ... > > fM(EL,3).*exp(-fM(EL,4).*(s.^2)*0.25) + ... > > fM(EL,5).*exp(-fM(EL,6).*(s.^2)*0.25) + ... > > fM(EL,7).*exp(-fM(EL,8).*(s.^2)*0.25) + fM(EL,9)).* ... > > sin(2*pi*s*R_el(EL))./(2*pi*s*R_el(EL)); > > > > RHO(iter) = quad(int_fun,0,1/dmax(iter)); > > clc;display(iter);display(numel); > > end > > RHO_t(numel,:) = RHO; > > end > > > > RHO_t(1,:)= 6*RHO_t(1,:); > > RHO_t(2,:)= 9*RHO_t(2,:); > > > > figure; > > axis([0.5 3.5 -10 10]); hold on; > > plot(dmax,RHO_t(1,:),... > > dmax,RHO_t(2,:),... > > dmax,RHO_t(3,:),... > > dmax,RHO_t(4,:),... > > dmax,sum(RHO_t,1)); > > title('Electron Density Profile'); > > legend('Fe','S','Fe1','Mo','Sum'); > > xlabel('d_m_a_x'); ylabel('Rho(r)'); > > set(gca,'XDir','reverse'); > > ############## > > > > Any suggestions will be appreciated. Thanks! > > > > Niu >
