[phenixbb] Composite omit map

Sam Tang samtys0910 at gmail.com
Sat Jun 3 12:00:03 PDT 2017

Dear Pavel

Thanks for the reply. I am trying to prove the presence of ligand as well
as to 'push' some density for the weaker part of the ligand. (This relates
to another thread I initiated.)  In short density for first part of ligand
is very good and can confidently be modelled but not the other part.

I have tried Polder Map as well as the conventional SA-OMIT map. My feeling
is that the conventional way gives better map for the ligand at the 'good'
region than Polder, but neither way improves density at the 'poor' region.

There seems less keywords to manipulate in Polder than in the conventional
way though.

Best regards


On 3 June 2017 at 21:44, Pavel Afonine <pafonine at lbl.gov> wrote:

> 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:
> http://journals.iucr.org/d/issues/2017/02/00/ba5254/ba5254.pdf
> https://www.youtube.com/channel/UCcdI0hfHngWAZLJWynxPQWg/videos
> Pavel
> 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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