[phenixbb] superpose CryoEM map onto an Xray map?
tim.gruene at psi.ch
Thu Oct 4 08:08:50 PDT 2018
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?
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
> 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,
> Vincent Chaptal, PhD
> MMSB -UMR5086
> Drug Resistance and Membrane Proteins Laboratory
> 7 passage du Vercors
> 69007 LYON
> +33 4 37 65 29 01
> phenixbb mailing list
> phenixbb at phenix-online.org
> Unsubscribe: phenixbb-leave at phenix-online.org
Paul Scherrer Institut
- persoenlich -
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297
GPG Key ID = A46BEE1A
-------------- next part --------------
A non-text attachment was scrubbed...
Size: 195 bytes
Desc: OpenPGP digital signature
More information about the phenixbb