Dear Brigitte,
Looking at the formulae it could be possible to get those results. Take an example below Rho_cal = -0.11, 0.0, 0.05, 0.05 Rho_obs = -0.08, 0.01, 0.04, 0.04 R-fac = 0.02/0.0 = undefined Correl = 0.0032 - (-0.0025*0.0025) -------------------------------------- = 0.99 sqrt(0.0043 * 0.0024) Did the calculations quickly so hope they are OK. However, I designed the data so that the denominator in the R-fac is zero i.e. the sum of Rho_cal = - sum of Rho_obs. It would imply that the ATMMAP from sfall does not cover the correct set of grid points for the ligand. You expect the Fc map to be positive in this region. You need to generate a new ATMMAP for each different ligand conformation. Adam Hi, I am trying to calculate real-space R-factors and correlation coefficients for an array of different ligand conformations to find out which fits best in experimental density. So far, I have been trying to use Overlapmap in CCP4 6.1.2 to do this, by correlating maps by residue and selecting the list a real-space R-factor option. I would like to compare a map with the ligand omitted to maps calculated with each ligand conformer. I am supplying Overlapmap with a refmac mtz file calculated without ligand in the model for map 1 and a pdb file that contains both protein and ligand coordinates to calculate map 2. However, I’m confused about the output. For the protein, which I know is well-defined and modeled correctly in the density, I see mostly reasonable correlation coefficients, ~0.9, but the real-space R-factor values are all over the place and range from zero to hundreds. For example, for one residue the correlation coefficient is 0.8309 with an R-factor of 210.333. I am very confused about how to interpret these values. Has anyone else tried to use Overlap for a similar purpose and could give suggestions as to what I’m doing wrong? Thanks! Brigitte
