[phenixbb] Composite omit map

Pavel Afonine pafonine at lbl.gov
Sat Jun 3 06:44:32 PDT 2017

I'm not sure I understand the concept of individual selection when doing 
composite OMIT map. The whole purpose of composite OMIT map is to do 
iterative omits and then put the entire mosaic back into full map so 
that each region of the map is "omit". This way you are expecting to get 
a less biased map that this map also may appear of a lesser quality.

It depends what question you are trying to answer. If you the question 
is to prove the presence of a ligand then simply compute Polder map:



On 6/3/17 19:48, Sam Tang wrote:
> Dear all
> Sorry for a very basic question about generating an omit map.
> I am trying to generate a SA-omit map for only my ligand but not the 
> protein core of my complex.  I presume I can use 
> phenix.composite_omit_map GUI and specify my ligand chain in Atom 
> Selection?
> All other parameters being the same, I notice that when I did not 
> select any atom the whole structure was divided to 30-40 regions but 
> when I selected my ligand chain it now divides into 89 regions. Is 
> there a reason why and is there any advantage to manually adjust the 
> number of omit regions?
> Many thanks and regards
> Sam
> Biochemistry Programme, School of Life Sciences, CUHK
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