Hi Deng,
> 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? > it's not unexpected for an OMIT map to appear worse than the original map. Indeed, it would be naive to expect the map to improve by removing atoms from model. If you add SA on top of it, this may (or may not, given stochastic nature of SA) degrade the map further, as SA is good at correcting gross model errors but not good for well refined near to final models. The purpose of OMIT maps is not to make your map look nicer, but to prove or disprove something, like questionable density (whether it is real signal, model bias or noise) etc. It also depends what you call "really bad". If you think the map looks worse beyond what one can expect from SA OMIT procedure, you may send us (Phenix) inputs necessary to reproduce the map you get and we will investigate. Pavel
