On Tue, Jan 31, 2012 at 12:04 PM, Xun Lu
I am refining a protein-DNA complex structure at 2.9A resolution. The R/Rfree is 0.2181/0.2501, which is pretty good, but I can tell that the DNA is not well refined. Some sugar puckers are not right. The distances between some base-paired bases are kind of short (~2.5A). I've tried including a reference model for the DNA, or including a cif file, and I've also tried to turn on the secondary_structure_restraints.... nothing worked. I must have not done it in a correct way. But how to do it? And how to deal with sugar puckers?
I don't know why the secondary structure restraints wouldn't work - could you please send me the PDB file off-list so I can see what's going wrong? (No data necessary.) By the way, which version of Phenix are you using?
In refmac, I can set the distances between bases during the refinement, so there must be a way to do it in phenix as well?
Yes, see here: https://www.phenix-online.org/version_docs/dev-973/refinement.htm#anch341 But hopefully the secondary structure restraints can be made to work. -Nat