[phenixbb] altloc non-bonded interactions

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Thu Aug 19 17:35:50 PDT 2010

Hi Paul,

> I have a structure at 1.1A with some interesting sulfate molecules
> that refuse to refine well.  I suspect two positions are alternately
> occupied by sulfate in some cases and two water molecules in others.
> I would like to refine with both (a sulfate and two waters) with
> each component at 1/2 occupancy.  With alternate conformations of a
> given sidechain, the two alternate locations automatically ignore one
> another w.r.t. non-bonded interactions.  However, different residues,
> it would seem, do not.

Could you send me the relevant parts from your pdb file? I'm having
a little trouble understanding your situtation.

Any atom with altloc A does not interact with any atom with altloc B,
no matter what residue(s) the atoms are in.


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