[phenixbb] full omit maps

Thomas C. Terwilliger terwilliger at lanl.gov
Fri Dec 29 11:29:25 PST 2006

Hi Jianghai,

The phenix full_omit map, if calculated with no model-building, is similar
to both the SFCHECK map and the CNS composite SA-OMIT map.

The phenix full_omit map removes atoms in each omit box and in a 2 A
radius around the omit box, then calculates phases, then puts all the
omitted regions together.  This is like the CNS SA-omit map with no
simulated annealing.  It is also like the SFCHECK OMIT map, except that
SFCHECK does not remove atoms 2 A around the box.

The real power of the full_omit map is to calculate it WITH iterative
model-building. In this case the atoms that get built inside the omit
region get an occupancy of 0.0 each cycle.  The model outside the omit
region gets better and better, so that the omit density gets improved
every cycle.  Then when all the omit regions are recombined, the map is
totally unbiased, but it can be much better than the starting omit map.

-Tom T

> Is this map a total OMIT map like SFCHECK does or a SA-OMIT map like
> CNS does?
> Jianghai

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