[phenixbb] Fo-Fo difference map for non-isomorphous datasets

[Pavel Afonine]

Hi Jordan,

Phenix implementation of Fo-Fo map calculation requires the data sets 
are isomorphous within some tolerance (which isn't large, I don't think 
6A will be tolerated!). Yes, there is quite involved and careful scaling 
happening as part of this procedure, which is important.

If you are subtracting real-space maps then you are on your own to do 
scaling. I'm guessing in real space scaling can be done more efficiently 
by doing it locally.

I'm curious to know how your or Tim's suggestions worked out in the end.

Good luck!
Pavel

On 3/9/19 01:21, Jordan Luke Pederick wrote:
>
> Hi,
>
>
> I am trying to generate a Fo-Fo difference map for two data sets of 
> the same protein at ~2.3 angstrom resolution. One dataset is native 
> and the other was soaked with a metal ion, so the purpose of the map 
> is for identifying and visualizing peaks that may correspond to a 
> bound metal ion.
>
>
> These datasets differ by 6 angstroms (~10%) along the A edge - an 
> isomorphous difference map generated in Phenix GUI wasn't useful
>
>
> As an alternative I was planning to make a real-space Fo-Fo difference 
> map making use of Superpose Maps in Phenix Gui as follows:
>
>
> Superpose maps would be used to superimpose (Fobs.metal, PHI.metal) 
> and (Fobs.native, PHI.native)
>
> The superimposed maps will be opened in Coot and a difference map 
> generated using "Extensions -> Maps ->  Make a difference map"
>
>
> There were two things I was unsure about:
>
>
> Does this seem like a reasonable alternative?
>
> Is scaling of the two datasets required before generating the 
> difference map?
>
>
> Cheers,
>
> Jordan
>
>

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