[phenixbb] superpose CryoEM map onto an Xray map?

vincent Chaptal vincent.chaptal at ibcp.fr
Thu Oct 4 07:23:55 PDT 2018

Hi Pavel,

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...

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 

It worked, with the 2 maps superposed that I can look and compare.

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 
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.

Please let me know if I'm doing something wrong as haven't yet invested 
into understanding map formats.

ps: Zhijie, thanks for the Chimera tip. I'll have a look into it later.

On 04/10/2018 12:00, Pavel Afonine wrote:
> Hi Vincent,
>> I am trying to superpose a CryoEM map onto a Xray map.
>> I tried the "superpose maps" under the map section of phenix 1.14 but 
>> it only takes "reflections" and not the .mrc format  of the CryoEM map.
>> should I transform the CryoEM map into structure factors using "Map 
>> to structure factors" or is there a better way to do this?
> 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 directly.
> Share your experience!
> Good luck,
> Pavel


Vincent Chaptal, PhD


Drug Resistance and Membrane Proteins Laboratory

7 passage du Vercors

69007 LYON


+33 4 37 65 29 01


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