[phenixbb] Refinement with partial model - question

Pavel Afonine PAfonine at lbl.gov
Fri Apr 2 10:40:58 PDT 2010

Hi Peter,

> Refinement of severely partial models can be greatly facilitated by 
> some way of describing the missing parts or at least knowing were 
> there is solvent and where protein.
> Some of these points are described in  "Refinement of severely 
> incomplete structures with maximum likelihood in /BUSTER-TNT"/ E. 
> Blanc 
> <http://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Blanc,%20E.>, 
> P. Roversi 
> <http://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Roversi,%20P.>, 
> C. Vonrhein 
> <http://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Vonrhein,%20C.>, 
> C. Flensburg 
> <http://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Flensburg,%20C.>, 
> S. M. Lea 
> <http://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Lea,%20S.M.> 
> and G. Bricogne (2004) 
> <http://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Bricogne,%20G.>/ 
> Acta Cryst./ (2004). D*60*, 2210-2221.

I agree. But if I remember correctly, they set up some a priori 
information in these areas and not just leave them empty. So when you 
let bulk solvent fill in these areas you assume that there is some 
density there, otherwise you assume that there is nothing there (which I 
guess is worse).


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