My bad! I've not had an excuse to take version 7 out on a spin yet.
Thanks for setting me straight Eleanor.
Dale Tronrud
On 5/9/2016 1:49 PM, Eleanor Dodson wrote:
> Well, Dale - you need the CCP4 GUI2!
> E
>
> On 9 May 2016 at 21:29, Dale Tronrud <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
>
> 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]>
> > <mailto:[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
> >
> >
>
>
|