[phenixbb] superpose CryoEM map onto an Xray map?

Pavel Afonine pafonine at lbl.gov
Thu Oct 11 09:28:23 PDT 2018

Hi Vincent,

> I am very lucky to see 2 maps of the same protein, at roughly the same 
> resolution, one by Xray and the other by EM (it's not that common). 
> The details from the 2 maps are however different...

wow, fascinating!

> Here is my procedure, please let me know what you think:
> - convert .mrc map to .mtz ; I get F, PHIF.
> - supperpose the maps:
> map1: labels 2FOFCWT, PH2FOFCWT
> map2: F, PHIF.
> I also provided the 2 PDBs as it is clearly stated on the input files 
> definitions.
> It worked, with the 2 maps superposed that I can look and compare.

Ok, sounds good so far. Yes, this is what I would expect!

> However, for some reason, the superposition has been done on chain C 
> and D of the crystallograhic model instead of chain AB (4 chains in 
> the asymmetric unit, making 2 dimers). Is there a reason there, 
> choosing the closest structure, best fit? (I see that it is possible 
> to define a superposition)

You can specify this manually!

> Another thing is that it creates a "supperposition in the middle", 
> meaning neither on model1 nor model2 from the input, and not a 
> crystallographic symmetric of model1. So I can't use the full 
> crystallographic maps, I have a "simplified" version of it.

I guess this is the feature of current implementation.


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