Hi Brigitte,
You are correct, the columns labeled Fobs and Fcal refer to density. The columns should be: averaged density for Obs and Cal for the main chain, then averaged density Obs and Cal for the side chains. I have included a version of overlapmap that calculates the R-factor correctly and have changed the above columns in the output.
All the best Adam
Hi,
I am using the program Overlapmap to calculate real-space R-factors and correlation coefficients in order to find ligand conformations that fit best within the density.
I'm confused by the Overlapmap output, which includes "Fobs" and "Fcalc" values that are used to calculate the R-factors and corr coeff. However, I'm not sure what these F values are as they should not be structure factors since the program seems to only deal with maps. Additionally, in many cases the Fobs and Fcalc values are either 0 or negative values, even for protein residues that are well-defined in the density.
Has anyone used this program before or have an idea of what could be going on here?
I have been supplying the program with a refmac mtz file with ligand unmodeled as map 1 and a pdb file with both protein and ligand coordinates to calculate the map 2.
Any suggestions or ideas of better ways to score ligand fits are appreciated, thanks.
Brigitte
I am using the program Overlapmap to calculate real-space R-factors and correlation coefficients in order to find ligand conformations that fit best within the density.
I'm confused by the Overlapmap output, which includes "Fobs" and "Fcalc" values that are used to calculate the R-factors and corr coeff. However, I'm not sure what these F values are as they should not be structure factors since the program seems to only deal with maps. Additionally, in many cases the Fobs and Fcalc values are either 0 or negative values, even for protein residues that are well-defined in the density.
Has anyone used this program before or have an idea of what could be going on here?
I have been supplying the program with a refmac mtz file with ligand unmodeled as map 1 and a pdb file with both protein and ligand coordinates to calculate the map 2.
Any suggestions or ideas of better ways to score ligand fits are appreciated, thanks.
Brigitte
overlapmap.f
Description: Binary data
