There may be several reasons.
1) Artefacts (some of them)
a) effect of mask: if there are large holes inside molecule and there
should be no electron density (for example hydrophobic holes) then in older
versions masks would put a constant density there and as a result difference
map would have negative densities. This has been dealt with in the newer version
b) Effect of TLS refinement. If you are using TLS then you can try without
TLS and compare densities. If it is effect of TLS then without TLS you should
not see negative density. TLS model is a simple model assumes that all atoms in
the group oscillates as a rigid group. Loops and other flexible parts may not
obey this assumption
2) Genuine density
Alternative conformations (Met almost always are in more than one
conformations). In these cases you may be able to see alternative conformation
if you look at very low level of electron density. And you may be able to see
if it is case by looking at the B values. If neigbouring atoms have large
differences in B values then it may be because of alt conformation
Regards
Garib
On 23 Nov 2011, at 07:54, Careina Edgooms wrote:
> 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
Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http://www.mrc-lmb.cam.ac.uk
