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

Tim Gruene tim.gruene at psi.ch
Sat Mar 9 02:47:15 PST 2019

Dear Jordan,

you can substract maps directly in Coot, and I would recommend this procedure 
to get the most reasonable out of it:

- superpose your two molecules with LSQ (not SSM), selecting the region of 
interest for the LSQ match
- transfer the map of the transformed molecule with the same operator
- check at a region where the density is decent that the two maps are on 
scale, i.e. make the level as level as possible with your scroll wheel. Most 
likely they are
- create the difference map, using the ratio of the two sigma-levels as 
weighting factor.
- do not overinterprete what you see

Best regards,

On Saturday, March 9, 2019 10:21:54 AM CET 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

Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

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