[phenixbb] occupancy

Pavel Afonine pafonine at lbl.gov
Wed Dec 22 22:12:54 PST 2010

  Hi Maia,

refinement of occupancies is probably the most documented topics in 


so your option number 1 is to check out this section of phenix.refine 

The option number 2 is to send me your PDB file and tell which atoms you 
want to relate as alternative conformations in occupancy refinement, and 
I will send you back a working example (or I will ask more questions 
off-list if your inputs are not sufficient to produce the unique sugestion).


P.S.: I will not have internet access all day tomorrow (Friday) till 
late night.

On 12/22/10 6:35 PM, Maia Cherney wrote:
> Hi phenixers
> I need to connect the conformation A to a ligand 1 and the 
> conformation B to a ligand 2. I need to get the group occupancies for 
> conformation 1 and ligand 1 (group 1) and group occupancies for 
> conformation B and ligand 2. I could not get the right groups 
> together. Your selections in the groups does not provide for 
> alternative conformations having different ligands.
> Could you help me?
> Maia

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