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 <[email protected]> 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 >
