[phenixbb] difference map based on the cryo-EM map

Pavel Afonine pafonine at lbl.gov
Thu Dec 1 08:04:20 PST 2016


> Supposed  by phenix.real_space_refine I got a PDB of protein-ligand, 
> will you please let me know how to get the subtraction map (difference 
> map?) which only show the density of the ligand, so that I can see 
> whether the ligand was well resolved in the map, or whether the built 
> ligand fits well with the ligand density?

it's not yet available (assuming you are asking for this to be done in 
real space). However you should be able to use your original cryo-EM map 
to infer this information.

Another alternative (which I can't dislike more) is to convert cryo-EM 
map into structure factors, run a round of phenix.refine refinement, and 
that will give you an MTZ with 2mFo-DFc and mFo-DFc map coefficients 
(which, by construction, will be model biased, unlike your original 
cryo-EM map!). How much sense they would make in this case that I can't 


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