[phenixbb] Simulated annealing omit maps

[SEKHAR1 at pitt.edu]

Hello friends,

I have a couple of questions regarding simulated annealing composite map
calculations.
(1)  Is there a way of specifying the percentage of residue co-ordinates
to be omitted each time as we move through the asymmetric unit?
I have found, when using CNS earlier, that depending on the structure,
the map quality often varies if you change this from the usual 5% to 4%
or even 3%, sometimes getting clearer.

(2) Does the 'number of boxes' you can specify in the GUI only affect the
fine structure/grid spacing of the map?  The map probably does not get
better all the time as we keep on increasing the number of boxes; when
do we reach the point of diminishing returns and what would be the best
way to estimate it?

Thank you very much and wish you all a Very Happy 2012.

K. Chandrasekhar