On Tue, Nov 22, 2011 at 11:54 PM, Careina Edgooms <careinaedgo...@yahoo.com> wrote: > 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?
It could mean that the sidechain is correctly placed, but poorly ordered, and the B-factor restraints are preventing the B-factors for those atoms from going as high as they probably should. I don't think this is terribly uncommon. I've seen it before, and each time I tried truncating the residue(s) to alanine, I got positive difference density back after refinement. If you see the same thing, my inclination would be to leave it alone and not worry about it as long as everything else looks sensible. The negative density around Met S could be radiation damage - also not uncommon, since these and carboxyl groups tend to get hit the hardest (unless you have heavier atoms). -Nat
