[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
>
>
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> phenixbb at phenix-online.org
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