[phenixbb] Omit map output map files

Manoj saxena mks131 at gmail.com
Mon Nov 16 19:22:11 PST 2015

Thanks to  Dr. Pavel and Dr. Fischmann for useful discussion and views on
Omit map,
and how to remove a possible bias.


On Mon, Nov 16, 2015 at 9:53 AM, Pavel Afonine <pafonine at lbl.gov> wrote:

> 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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