Solving a structure: Tips and Tricks
From CCP4 wiki
One possible way of improving "weak density" is to improve the model as much as you can: make sure you modeled all alternative conformations, all solvent, etc.
- B-factor sharpening may help, although keep in mind that it will enhance the noise too.
- Other options: kick maps, omit kick maps, b-factor sharpened kick maps... available from Phenix
- You can try GrowDensity method (Acta Cryst. (1997). D53, 540-543) which is available as phenix.grow_density. This is still under (slow) development, so if you decide to go this route than the Phenix developers can help with the details.