Hi everyone,
I am working with protein-ligand complex structure. For the head group in one of the ligands in the structure, two more positions in addition to the current position look possible according to the blue density in Coot. I am thinking of assigning multiple occupancies/positions to this head group. So, I am wondering what I should do to achieve this. Is the following strategy right?

1. Fit the head group to the density at three different positions separately in Coot and save them separately.

2. Find out the atoms that are different among the three ligand positions and combine the same atoms with different positions and change the occupancy of those atoms to something between 0 to 1.

3. Use Phenix. refine to refine. The occupancy refinement should be automatically on, right?
Is this the best way to assign multiple occupancies/positions to the head group? Thank you so much!

Also, anything to look after refinement which can tell me whether I am assigning the right multiple conformations to the ligand?

Thank you so much!

Best,
Wei