Would an omit map calculated after removing the ssDNA from the model and then gently randomizing the remaining coodinates using the NOISE option in pdbset (possibly not in the GUI version)
NOISE [maximum_shift] [subkeys] Introduce random shifts into atom positions in orthogonal coordinates. maximum_shift maximum shift (Angs) defaults to 0.2 Angs, fails if greater than 0.5 Angs be a possible alternative to a simulated annealing technique? Would it not be similarly effective at removing any memory bias in the remaining coodinates, and very easy to do? Having said that, it is usually simplest to do what the referee requests, if at all possible. And if your DNA isn't there in the omit map, then you have no reason to suggest that it is there at all. best wishes Pete On 4 Nov 2013, at 18:02, Mark Brooks <[email protected]> wrote: > 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 > Prof Peter Artymiuk Krebs Institute Department of Molecular Biology & Biotechnology University of Sheffield Sheffield S10 2TN ENGLAND
