Can someone tell me what the number is that appears with each residue above the bar in the COOT Density Fit Analysis graph?
I have a structure with good data (resolution=2.3A, Rmerge=5%) but a high Wilson B of ~60. The structure refines reasonably well; we've gotten the Rfactor to 18% and Rfree to 22%. It's a previously determined structure (with new ligands) so we know there is no gross mis-tracing. If I perform the Density Fit Analysis in COOT, I get a poor looking plot with significant numbers of red and orange bars. Hovering over a bar gives the residue and a number that is pretty low (seldom above 0.7) and in several places there are long stretches of residues that appear fine in the density where the number in this plot is 0.3. I see from the documentation and prior CCP4bb postings that perhaps this results from poor scaling and that I can change the colors of the bars with the (set-residue-density-fit-scale-factor X) command. If I use the recommended scale factor (1/4*sigma), the bars get redder. Doing so also changes the colors and the size of the bars but not the number that appears above each bar. My question then is what is the number that appears in this plot? Is it a correlation coefficient? I have calculated the per residue correlation coefficients with the CORRELATE program and see much more reasonable values. Thanks for any suggestions. Andy -- Andrew M. Gulick, Ph.D. ----------------------------------- Hauptman-Woodward Institute -----------------------------------
