Sounds like your refinement is failing probably because of the low data:parameter ratio at this resolution and/or the composition of your asymmetric unit, poor initial phase information (probably a molecular replacement solution which is close, but still far from the truth either in sequence composition or atomic configuration).
In these cases, it is useful to use a reference structure containing an idealized A-form (RNA) or DNA helix with the *correct* sequence composition and ensure that the refinement program matches the residues appropriately upon the start of refinement. If you've got some strange tertiary architectures (k-turns, gnra tetraloops or some other non canonical motif), include those as well. Then, there is the issue how the restraints are generated for refinement, I've found autoBUSTER's LSSR regime (based on interatomic distances as opposed to dihedral angles) to be quite good at restraining the refinement, but that's my own opinion on a few particularly challenging cases. As a polishing step (and if you have to revert to real space refinement), the rcrane plugin but Kevin Keating is very helpful. It is accessible within coot. F On Apr 16, 2015, at 8:22 AM, Almudena Ponce Salvatierra <maps.fa...@gmail.com> wrote: > Dear all, > > Despite molprobity analysis tells me my structure contains no puckers that > are wrong, the pukka puckers tool within coot lists a number of them with for > example inconsistent distance bewteen the phosphates. > > I would like to ask if any of you have dealt with this before, and how does > one "make consistent" the distance between phosphates with the sugar > puckering? Only by direct space refinement? Or is there a way to change > something else... > > My structure is a 3 A resolution so I can definitely see the backbone of the > nucleic acid chain but for sure I can not tell whether the pucker was > assigned properly or not from the electron density. > > Any ideas? > > Thanks a lot in advance. > > Best wishes, > > Almudena. > > -- > Almudena Ponce-Salvatierra > Macromolecular crystallography and Nucleic acid chemistry > Max Planck Institute for Biophysical Chemistry > Am Fassberg 11 37077 Göttingen > Germany >
