[phenixbb] Symmetry of map vs Symmetry of model

Pavel Afonine pafonine at lbl.gov
Fri Jul 26 23:00:22 PDT 2019

Hi Pramod,

let's think of it this way.. Your experimental map (that you call a 
weird name "volume")  is the experimental data, or at least the data 
that is as close to experimental as you can get at this stage (unless 
you go back to 2D images).

Now if you enforce symmetry on the data, that means you wipe out lower 
symmetry information, there is no obvious reason why atomic model that 
you fit into these data should deviate from the symmetry that you 
enforced on these data.

So the answer is: if data was symmetrized (enforced to have a particular 
symmetry) then the mode MUST have that symmetry too.

Phenix has tools to make sure this happens.

Good luck,

On 7/26/19 13:46, pramod kumar wrote:
> Dear all,
> I have a query related to symmetry imposition and corresponding 
> tweaking of model.
> If symmetry (say, C4) was imposed during the reconstruction of a 3D 
> volume, does symmetry also need to be imposed when building the atomic 
> model (say, in Phenix)? Or could this constrain be relaxed?
> Do we need to tweak the model in Coot for other chains or since it is 
> build on symmetrical partners therefore should only be made in one 
> chain and copied for all without any fitting?
> Pramod Jaykar, Ph.D.
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