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What does a straight difference map look like? i.e. omit one nucleotide at a time, do a few cycles of refinement and then inspect the weighted difference map - SA may be too violent for your structure.
Eleanor
On 4 Nov 2013, at 06:36, dengzq1987 wrote:

Dear all,
 
 Recently, I received the comments from referees, they asked for the SA-omit map of the ssDNA of our protein-DNA complex. They said that simulated annealing omit map better than a biased 2Fo-Fc. The ssDNA consists of seven thymidine nucleotide. Our data diffracted to 2.65A，but the data quality is not good and twin. We tried to produce SA-omit map using phenix. The map is really bad. Does anyone have suggestion to refine the map?  Thank you!
 
 
Bests,
zq Deng
2013-11-04
dengzq1987