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Re: [ccp4bb]: sigmaa weighted fo-fc omit map
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youngsoo kim wrote:
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> Dear all,
> I would like to have some help to figure out what is going on difference
> maps. The apo structure was solved at 1.8 A and well refined. A ligand
> from a co-crystal was easily located by fo-fc omit map using the
> apo-structure. The fo-fc map is very clean and good enough to fit the
> ligand. After all the refinement of the ligand into the co-crystal
> structure, the sigmaa weighted fo-fc omit map was calculated, but it
> is much worse that the starting fo-fc omit map.
Why not do the sigmaa map in the first place ?
Possible intereptation of result:
If by 'worse' you mean the apperance of negative peaks (rather than
maybe the ligand has occupancy lower than 1.0. If peaks are positive and
I guess you should try to model it in an alternative orientation ...
If you do some refinement of the structure without the ligand
and then an mFo-DFc map, this must give you clearer density.
'Personal bias' suggestion:
At that resolution, the refinement can be done with an ARP/wARP run (mode
This will give better results, by placing 'free' atoms to ligand density.
Evemore, you could try to use 'mode warpNtrace' which will rebuild
-hopefully- most of the structure,
getting rid in a much better way of 'previous model bias'. Never done it
myself but at
least Hans Parge told me he is doing that in an almost regular basis for
with very good results.