[phenixbb] some sort of occupancy refinement

Kendall Nettles knettles at scripps.edu
Thu Dec 31 15:25:42 PST 2009

Are you saying that your ligand can adopt two completely separate conformers, or that part of it moves around? Either way, you do want grouped refinement with the altloc, either on the whole or part of the ligand that is different. Altloc automatically performs group refinement. It doesn't make physical sense to do otherwise, as you are essentially assigning a percent that the ligand is in the different conformers, rather than saying that part of the molecule is only there part of the time.

Happy New Year,
Kendall Nettles

On 12/31/09 5:41 PM, "Bryan W. Lepore" <Bryan.Lepore at umassmed.edu> 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?


p.s: Happy New Year with Blue Moon Eclipse (~10degW->180degE long. eastern

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