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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.

General comment:
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
positive)
maybe the ligand has occupancy lower than 1.0. If peaks are positive and
negative
I guess you should try to model it in an  alternative orientation ...

Suggestion:
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
molrep).
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
protein/ligand structures,
with very good results.

        Tassos