[phenixbb] Phenix omit maps

[Dorothee Liebschner]

Hello Wolfram,

is the output of phenix.maps with maps.omit.selection=(resname LIG)
> equivalent to removal of LIG atoms from coordinates and subsequent map
> calculation with an empty maps.omit.selection?
>

This is correct, both steps are equivalent. If something is indicated for
maps.omit.selection, it will be removed from the model to calculate the
omit map. So it is the same as using a pdb as input, where the selection
was deleted.


> What, if any, measures of bias removal are applied in the process of map
> calculation, absent any explicit efforts by the user to modify coordinates?
>

Phenix.maps is a map calculation tool, so there are no additional steps,
such as refinement or modification of coordinates. What kind of bias
removal were you referring to?

I hope I could answer your question,

Best wishes,

Dorothee

On Fri, Mar 4, 2016 at 9:28 AM, wtempel <wtempel at gmail.com> wrote:

> Hello all,
> is the output of phenix.maps with maps.omit.selection=(resname LIG)
> equivalent to removal of LIG atoms from coordinates and subsequent map
> calculation with an empty maps.omit.selection?
> What, if any, measures of bias removal are applied in the process of map
> calculation, absent any explicit efforts by the user to modify coordinates?
> Thank you,
> Wolfram Tempel
>
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