Hi Tommi, 5-6 A is a tough resolution so don't expect things easy with any method or software package. Plus, methods (eg., density modification, refinement, model building) are typically optimized towards higher resolution. But with some luck and effort, you can make it work. Some suggestions that are appropriate to try at this resolution: - if NCS is present, try NCS constraints vs restraints, and see what works best; - optimize coordinate and B factor weight if Rfree-Rwork gap is overly large or geometry is poor; - use all possible information (if available): reference model restraints, secondary structure restraints (with careful manually-verified annotation of SS), Ramachandran plot restraints; - if model needs some substantial movement to fit the map, try Simulated Annealing; - try density modification to see if you get a more interpretable map that can help you to build a better model (Tom can correct me, but I thought NCS averaging happens as part of DM). This is all I can think of... Pavel
Hello all,
I was wondering what would be current best protocols for trying to improve maps/phases for low resolution MR / refinement solutions (5-6 Å resolution).
High solvent content of course, dimeric 2:2 protein complex so some NCS averaging and density modification I assume might help (related structures known, currently maps very blobby, clear solution but I think should be able to do better...).
Also, refinement suggestions welcome.
Best route in phenix? So far worked initially with ccp4. Other suggestions also welcome.
Thanks! Tommi