[phenixbb] (no subject)

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Wed Dec 2 12:55:26 PST 2009

Hi John,

> I am looking for advice on how to best refine the structure of a complex that
> has one component that can adopt two completely different conformations (a DNA
> duplex).  I can model both conformations and set occupancies to 0.5, and try to
> constrain_group their occupancies, but in phenix.refine the two conformations
> are interpreted as major clashes.

The trick to avoid the clashes is to set the "altloc" characters in
column 17 of your PDB file. E.g. assign "A" to all atoms of the first
conformer, and "B" to all atoms of the second.

phenix.refine should correctly interpret your PDB file if you have
a whole chain with altloc A followed by a whole chain with altloc B,
assuming the chain id is identical and there are no TER cards between
the conformers.


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