[phenixbb] altloc non-bonded interactions

Pavel Afonine pafonine at lbl.gov
Thu Aug 19 22:04:30 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.

you can do this in phenix.refine by assigning the same residue number to 
sulfate molecule and these two waters, and assign different altloc 
identifiers to them  (say altloc A to sulfate and altloc B to waters). 
The rest phenix.refine will figure out automatically. The values of 
initial occupancies can be any.

Let me know if you need more help with this.


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