Dear All,
Thank you very much for valuable suggestions and educating me on the normal mode refinement. Actually, I am trying to refine a protein (cytosolic domain and trans-membrane domain). I found a solution through PHASER and density looks really good in both domain but as i proceeds with refinement density remain great in both domain till Rfree around 38%. Interestingly, with further refinement cycle, Rfree reduced to 30% but the density in the trans-membrane domain becomes very weak. That is why i am wondering whether it is possible to improve the density in the trans-membrane domain by using Normal mode refinement. Conservatively speaking, it could be possible that trans-membrane is highly flexible or disordered and after much cerebration, i am thinking to incorporate the normal mode refinement to monitor if there is any improvement in electron density trans-membrane domain.
I would follow suggestions of Dr, Mande and Dr. Ethan. Also, would give a try to what Arpita has suggested. I further, warmly welcome any suggestion on refinement procedure to improve electron density in flexible or disordered trans-membrane domain.
Appu