[phenixbb] occupancy of a part of a ligand

Pavel Afonine PAfonine at lbl.gov
Wed Feb 10 09:03:25 PST 2010

Hi Maia,

yes, Young-Jin is right, you can do it in phenix.refine. Use either 
"refine.occupancies.constrained_grouop.selection=" or edit altloc fields 
in the PDB file so phenix.refine sees them as two alternatives.

Let me know if you need more help with this.


On 2/10/10 8:37 AM, Maia Cherney wrote:
> Hi Pavel,
> I have a ligand (ADP or ATP) that partially lost the last phosphate 
> group. Can I refine a group occupancy for the adenosine part of the 
> ligand separately from the phosphate groups of this ligand. If I do 
> atomic occupancies, they diminish for the terminal phosphate groups. I 
> can imagine that I can refine them as two superposed ligands with 
> different numbers of phosphates, but is it possible to do just 
> different group occupancies for parts of the ligand?
> Maia
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