[phenixbb] superpose CryoEM map onto an Xray map?

Pavel Afonine pafonine at lbl.gov
Thu Oct 11 07:14:48 PDT 2018

Hi Sean,

> Hello I just want to follow up on this question as I have a similar 
> one, namely I would like to align two cryo-EM maps.

This is what I replied last time:

you can try.. Yes, convert both maps into Fourier space equivalents and 
feed into the program. Note, you need  two models that fit two maps. The 
way it works is that it superposes models first, then applies 
corresponding operators (that superpose models) to maps. I can't 
remember anyone asking this questions before on this list or myself 

I did not hear any feedback re whether this worked or not. If this does 
not work we may think of a new tool to do this!

> I have the conversion of the individual mrc files to mtz file working 
> fine using the “map to structure factors” gui.  However if I use 
> “Superpose Maps” the resulting PDBs and maps are shifted away from the 
> inputs.  Is there anyway to have the maps in the “reference frame” of 
> the first input model/map? I know this is easier in Chimera but I am 
> worried that the resampling in chimera might introduce some errors 
> that could be avoided if done in using the mtz files in Phenix (maybe 
> this is an incorrect worry though and my question irrelevant?).

Map superposition requires interpolation, as well as resampling if they 
are not on the same grid. Both can introduce deviations from original 
map. Where this deviation is significant or within the noise -- I don't 
know, but if I guess I'd say it is not significant.


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