Dear Jerome,
some ideas to check:
- MD: you probably mean MR (molecular replacement)
- before starting refinement, if you found a solution by MR, did you look at the structure, crystal packing etc., no big clashes between molecules?
- related with that, did you validate the space group? Run several MR's with different space groups (which make sense from indexing) and compare the results
- refinement: run simulated annealing (initially with rather high temperatures, later in refinements at lower temperature), this helps to get out of local energy minima; energy minimization is done as part of that also
- include hydrogens in the refinement, this reduces clashes throughout the structure (they are added as riding hydrogens, i.e. predicted from geometry, they don't need to be resolved in the map for that)
- check your atomic model and do model building, e.g. in Coot, use Ramachandran restraints etc., go through the structure and refine manually, reinject that model into Phenix for further refinement; iterate; check whether your map improves
- run composite omit or polder maps if you have doubts about some regions, e.g. to figure out a loop conformation etc.
- is the diffraction isotropic? i.e. does the crystal diffract equally well in all directions? anisotropic diffraction can make refinement more difficult, but it can be corrected for
- use the phenix.predict_and_build tool to improve your AlphaFold prediction and refine your atomic model, see https://phenix-online.org/documentation/reference/alphafold.html
Best,
Bruno
-----Original Message-----
From: JEROME JOHNSON via phenixbb