Maybe try CNS or SFCheck:

http://groups.yahoo.com/neo/groups/cnsbb/conversations/messages/1720

 

To improve Phenix maps, maybe try increasing the number of boxes (the parameter IIRC "n_box_target=" )

http://www.phenix-online.org/documentation/autobuild.htm

 

In CNS, you can decrease the starting temperature in the annealing section, to reduce the 'violence' of the simulated annealing:

http://cns-online.org/cgi-bin/cns_solve_1.2/cns_view.cgi?&file=inputs/xtal_refine/composite_omit_map.inp

----------------------------------->8-------------------------------Snip------------------------------8<------------------------------

{* starting temperature *}
{===>} temperature=500;

----------------------------------->8-------------------------------Snip------------------------------8<------------------------------

 

As said elsewhere, if your map is still poor, maybe it's trying to tell you something...

 

Mark

 

 

 

 

On 4 November 2013 06:36, dengzq1987 <[log in to unmask]> 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

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dengzq1987