Good morning CCP4 members I have a question about a 2F0-Fc difference map that I calculated with Refmac. In some instances it gives me negative (red) density around part of a side chain and no positive density in sight. Furthermore the entire residue fits well into the blue density of the complete map, including the part with negative density.
I am struggling to interpret this. Does the fact that it fits the blue density mean that the side chain is in the correct place or does the red blob on part of the side chain (eg on the sulphur in a Met residue) mean that something funky is happening with this side chain? Thanks for any assistance Careina
