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, Tim 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 GPG Key ID = A46BEE1A