[phenixbb] Omit map

Pavel Afonine pafonine at lbl.gov
Tue Nov 22 22:01:08 PST 2011

Hi Rajesh,

model bias, in a nutshell, is when you see something in the map that is 
conveyed by the model (that may not be correct) and not by the data.

I am not sure how one can get an idea about model bias looking at 
triplet of numbers: Rwork, Rfree and Molprobity percentile. By the way, 
your Rwork/Rfree look pretty good (given the 2.7A resolution).

Anyway, if everything else: bunch of model and data statistics, local 
and global model-to-data quality fit all look well (*), and you are 
still suspecting something isn't right, then you can invest from a few 
days to a week or so into computing an "Iterative Build OMIT map" as 
described here:

Iterative-build OMIT maps: map improvement by iterative model building 
and refinement without model bias. T. C. Terwilliger, R. W. 
Grosse-Kunstleve, P. V. Afonine, N. W. Moriarty, P. D. Adams, R. J. 
Read, P. H. Zwart and L.-W. Hung Acta Cryst. D64, 515-524 (2008)

This map is supposed to be bias free.


(*) For more details see here:

> I have a structure 2.74 A structure with R/freeR 22.7/27.9%. But the 
> molprobity score is 50th percentile.
> If I fix the outliers they wouldn't go away and molprobity score 
> remains same or get worst.
> This structure was solved by molecular replacement using a bacterial 
> protein with 38% identity.
> I am wondering if there is an model bias? I have not identified 
> particular region in model for bias.
> My questions are: Am I right in thinking if there is model bias based 
> on above info?
> I  added my .pdb and .mtz and do SA-composit omit map. This is running 
> from morning and I have feeling that I will get results after 
> thanksgiving. Is this the correct way of doing a omit map for the 
> purpose I mentioned?
> I saw lot of discussions on omit map but couldn't grasp everything and 
> I am sure same questions might have been asked before.
> I have couple of classical papers next to me but I need help. I would 
> appreciate if you could help me out either suggesting me how and what 
> to do or pointing to previous thread over the this BB.

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