You can also calculate an Fo-Fo map, phased with a model with the
active site removed. This map is more cumbersome to calculate with CCP4
than Phenix. The interpretation of this map is complicated when you are
replacing one ligand with another, but it will clearly (one hopes) show
that there is a change that is due to a difference in the diffraction
and will not be biased toward either model.
Dale Tronrud
On 5/9/2016 1:15 PM, Eleanor Dodson wrote:
> I think it is enough to do several (20? 50?) cycles of refinement of
> the isomorphous structure, without its ligand, against the new data.
> Keep the same FreeR
>
> Then see if your new ligand looks clean and undistorted by the old one -
> there must be difference I presume?
>
> Eleanor
>
> On 9 May 2016 at 14:38, Armando Albert <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> Dear all,
> We would like to provide a section of an unbiased electron density
> map to illustrate de correctness of a ligand conformation.
> What shall we do using CCP4?. Do I have to recalculate the electron
> density after the first round of refinement just after the molecular
> replacement?.
> This could be useful but the model is isomorphous and also contains
> a similar ligand, so even if I delete it the protein structure would
> be "affected" by the ligand.
> Thank you for your suggestions in advance
> Armando
>
>
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