[phenixbb] some sort of occupancy refinement

Pavel Afonine PAfonine at lbl.gov
Fri Jan 1 01:30:23 PST 2010

Hi Bryan,

I'm not sure I understand what exactly you are trying to do (at least at 
this time), but if you send me your PDB file and tell me what exactly 
should happen to its content during refinement, then I will most likely 
send you an example of how to do it.

The past experience shows that this kind of questions is usually 

Happy New Year!

On 12/31/09 2:41 PM, Bryan W. Lepore wrote:
> question is after the setup here :
> i have a ligand with multiple conformers.  i gave each conformer a 
> different chain label.  refining occupancy for the overlapped parts 
> kicks that part out of the density.  i have remove_selection for the 
> parts that are 1.0 and they seem OK.  a single conformer stays in the 
> density.  i tried starting with and without site or occupancy 
> refinement, no help.
> i do not want group occupancy refinement b/c some parts do not overlap 
> - i.e. they "should" be occupancy 1.0 -- i tried it anyways with 
> constrained_group =... to check.
> is the chain label an improper way to do this?
> -bryan
> p.s: Happy New Year with Blue Moon Eclipse (~10degW->180degE long. 
> eastern HS)!
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