Hi Quixu, I also used phenix.refine with the "reference model" ( I have high > resolution model for one domain of the low resolution protein) and > "secondary structure restraints", but it seams the same. Any suggestion? > > BTW, is that simulator annealing not suitable for low resolution structure? > I used the simulator annealing method of CNS and phenix.refine, but the > geometry of the structure is always destroyed seriously.
using the latest phenix.refine from nightly builds ( http://www.phenix-online.org/download/nightly_builds.cgi), try combined strategy: - refinement of individual coordinates and ADPs, and - use SA (try different temperatures, say 5000K and 10000K), and - use reference model, and - use weight optimization which is not much improved in the latest nightly builds and can use multiple CPUs, and - use Ramachandran plot restraints, and - if NCS is available - use it. Make sure you use it in torsion angle space (this is a new option that is much more robust and does not require ad hoc decisions about NCS group selections) - use secondary structure restraints ONLY IF a) they are determined automatically from non-distorted starting model that has good geometry, or b) manually with great deal of thought, and - try using H atoms although they may not help much f you are far far away from a final model. When exploring the maps use automatically sharpened maps which typically enhances the weak features on low resolution map. Combining sharpening with map kicking should further improve the maps. Some experimenting with the above options might be helpful. If this doesn't help then please contact me *off-list or at phenixbb* and I might be able to help. Pavel.
