[phenixbb] Omit map output map files

[Pavel Afonine]

Hi,

> What Pavel describes is how to get a “difference map”. But it is not 
> an “omit map” per the original definition.
>

perhaps we are getting into terminology here.. I'm sticking to the 
original paper by T. Bhat.

Difference map is F1-F2, F1=w1*Fobs, F2=w2*Fmodel. I believe you can 
prefix it with "omit" if you omit something (remove part of model) from F2.

> The omitted part should never have been part of the model during any 
> refinement step before the omit map is calculated. The purpose is to 
> prevent bias.
>

This is where it gets into nuances not discussed in the original paper, 
if memory serves.

> If the model has already been refined with a ligand, then the 
> technique of simulated annealing refinement can be used to remove the 
> bias after removing the ligand. This approximates an “omit map” (still 
> one may argue not a real “omit map”, but close enough).
>

Yes, this seems to be the common mindset. But I'm yet to see a 
convincing example with clear illustration of such bias. I believe this

1) remove ligand;
2) do some refinement (optionally, don't believe really necessary!);
3) compute mFo-DFc map;

should be good enough in most cases.

Pavel

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