Just a few quick comments for clarification:
It seems like Autobuid uses the nomenclature DA, DC, DG and DT for the DNA bases while Phenix.Refine either doesn't like the nomenclature or the restraint files uses a different one. It still however lets me do the refinement...although I don't know if it just ignores the DNA part. Can someone enlighten me on this.
phenix.refine understands the whole variety RNA/DNA names. The DA, DC, DG, DT names have been the standard PDB names as of summer 2007.
Also, the nomenclature Coot seems to like is Ad, Cd, Gd, Td for the DNA
These are older monomer library names; they've never been a standard.
and doesn't like the above phenix style.
Paul Emsley knows best, but I believe current Coot versions understand the 2007 standard PDB names, too. Ralf