Hi Wei,

as long as your PDB file models altlocs like this:

ATOM   5085  N  AALA   270      19.772  -6.267  40.250  0.75  5.17
ATOM   5086  CA AALA   270      19.927  -5.299  41.342  0.75  5.15
ATOM   5087  CB AALA   270      20.132  -6.108  42.617  0.75  6.92
ATOM   5088  C  AALA   270      21.058  -4.290  41.124  0.75  5.06
ATOM   5089  O  AALA   270      20.831  -3.090  41.384  0.75  5.54
ATOM   5090  N  BALA   270      19.733  -6.282  40.242  0.25  5.04
ATOM   5091  CA BALA   270      19.592  -5.512  41.492  0.25  5.03
ATOM   5092  CB BALA   270      19.702  -6.389  42.726  0.25  6.62
ATOM   5093  C  BALA   270      20.673  -4.426  41.454  0.25  4.77
ATOM   5094  O  BALA   270      20.381  -3.268  41.761  0.25  5.70

it's going to work in phenix.refine automatically. See more details here:
http://phenix-online.org/documentation/refinement.htm#anch111

However placing a TER record between conformers 

ATOM   5085  N  AALA   270      19.772  -6.267  40.250  0.75  5.17
ATOM   5086  CA AALA   270      19.927  -5.299  41.342  0.75  5.15
ATOM   5087  CB AALA   270      20.132  -6.108  42.617  0.75  6.92
ATOM   5088  C  AALA   270      21.058  -4.290  41.124  0.75  5.06
ATOM   5089  O  AALA   270      20.831  -3.090  41.384  0.75  5.54
TER
ATOM   5090  N  BALA   270      19.733  -6.282  40.242  0.25  5.04
ATOM   5091  CA BALA   270      19.592  -5.512  41.492  0.25  5.03
ATOM   5092  CB BALA   270      19.702  -6.389  42.726  0.25  6.62
ATOM   5093  C  BALA   270      20.673  -4.426  41.454  0.25  4.77
ATOM   5094  O  BALA   270      20.381  -3.268  41.761  0.25  5.70

will result in phenix.refine refining group occupancy of each conformer individually.

Pavel

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 


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