[phenixbb] assign multiple ligand conformations

Pavel Afonine pafonine at lbl.gov
Tue Feb 11 08:18:44 PST 2014


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
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

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