Straightforward in Refmac...(a CCP4 package)...
From my iPhone
On 6 May 2014, at 18:02, "Chris Fage" <[log in to unmask]> wrote:
> Hi Everyone,
>
> In my 2.5-angstrom structure, there is negative Fo-Fc density
> surrounding a metal ion after refining in Phenix. From anomalous
> diffraction I am certain of the metal's identity and position in each
> monomer. Also, the ion is appropriately coordinated by nearby side
> chains. Should I be refining the occupancy of the ion in attempt to
> "flatten" the negative density? I am considering soaking the metal ion
> into crystals or cocrystallizing and collecting additional datasets.
>
> Thanks for your help!
>
> Regards,
> Chris
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