[phenixbb] superpose CryoEM map onto an Xray map?

Tim Gruene tim.gruene at psi.ch
Thu Oct 4 08:08:50 PDT 2018


Dear Vincent,

in case you have PDB files, one for each map, you could superpose model
1 onto model 2 and make the map 1 follow the same transformation. I
believe that this can be done with Coot. Does this work for your purpose?

Best regards,
Tim

On 10/04/2018 04:23 PM, vincent Chaptal wrote:
> 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
> definitions.
> 
> 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
> superposition)
> 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.
> Thanks
> Vincent
> 
> 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
> 
> MMSB -UMR5086
> 
> Drug Resistance and Membrane Proteins Laboratory
> 
> 7 passage du Vercors 
> 
> 69007 LYON
> 
> FRANCE
> 
> +33 4 37 65 29 01
> 
> http://mmsb.cnrs.fr/en/
> 
> 
> 
> 
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-- 
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Tim Gruene
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