[phenixbb] kickmaps

Veronica Fiorentino veronicapfiorentino at gmail.com
Fri Nov 25 03:24:13 PST 2016

> Dusan's "kick maps" idea has evolved into something better (we hope) that we
> call FEM (Feature Enhanced Maps)[*].
> Reading is available here:
> Let us know should you have any questions or problems!

Thanks a lot. I did use FEM and they look good.
My real aim: In my structure there is a loop that looks complteley
different to homologus published PDB structures. Can I use a FEM (2mFo
-Fc) and show the density at  2Sigma to prove that my loop is distinct
and real (away from model bias). I also made a
AutoBuild-Iterative-Buiild-Composite-Omit-Map that produced a
resolve-composite-map.mtz (shows same loop density). What sigma level
should I display these maps in a paper?

I did look at pavel_maps.PDF but confused as there are so many
numbers. Thanks a lot.


> Pavel
> [*] This is still experimental and ongoing. Significant improvements to this
> tool are envisaged in future.
> On 11/24/16 09:29, Veronica Fiorentino wrote:
>> Dear all,
>> I am using the latest Phenix; Calculate Maps does not seem to have an
>> option to for kickmaps as given in the
>> https://www.phenix-online.org/documentation/reference/create_maps.html
>> I have made a screenshot:
>> http://imgur.com/a/upgqy
>> Am I missing something obvious? Alternately, If anyone can share a
>> script I would prefer it!
>> many thanks
>> Veronica
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