[phenixbb] Water/residue alternative conformations

Roeland Boer rbocri at ibmb.csic.es
Fri May 29 00:58:38 PDT 2009

Dear all,

I'm refining a 1.45 Ang structure in which I have several residues that
have alternate conformations. These alternate conformations in some
cases coincide with additional density that suggests the presence of a
water molecule, appropriately positioned to make hydrogen bonds with
near atoms. I have modeled partially occupied waters in these additional
densities and linked their occupancies with the alternate conformation
that is not clashing with the water in question. My problem is that
these partially occupied waters are pushed away by the 'overlapping'
alternate conformation of the amino acids. I guess there's an antibump
restraint somewhere? How can I tell phenix that these alternate waters
are not sterically clashing with the amino acid (since the sum
occupancies of the water plus alternate conformation is 1)?

The attached image shows one of those disordered residues after
refinement. Water 1519 is pushed away from one alt conf (A) of Gln13,
whereas the density suggests it should be making a hydrogen bond to OE1
of the altconf B of Gln13.

I describe the occupancies of the situation in the attached image as below.
refinement {
    refine {
      occupancies {
         constrained_group {
          selection = chain A and resseq 13 and altloc A
          selection = (chain A and resseq 13 and altloc B) or (resname HOH
and resseq 1519 and altloc A)

Roeland Boer.

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