[phenixbb] Clashing alternative conformations

Ralf Grosse-Kunstleve rwgrosse-kunstleve at lbl.gov
Thu Dec 1 14:31:32 PST 2011

Hi Sozanne,
The rules for alt. confs. are such that a-a and b-b will always clash. Let
A,B chain labels, and a,b,c be altloc labels. You could assign A-a, A-b for
the two conformers in chain A, and B-a, B-c for the two conformers in chain
B. This way the second conformers will have no nonbonded interactions.
(The general rules are: blank-x interact, x-x interact, x-y do not

On Thu, Dec 1, 2011 at 2:13 PM, Sozanne Solmaz <ssolmaz at mail.rockefeller.edu
> wrote:

> Dear all,
> I have the following problem: I have a homodimer of two protein chains A
> and B, which I refine in Phenix, and one residue has 2 alternate
> conformations (a and b) for each chain.  If the  residues of both chains A
> and B are in the alternative conformation b, they clash. However, I would
> expect that never both residues are in conformation b, and therefore only
> the combinations aa, ab and ba of alternative conformations exist. My
> problem is, that during the refinement, the two b conformations of the
> residues clash, which drives the clash-score of the overall structure to a
> very high value  and repulsion pushes the two b-conformations apart during
> refinement, therefore I cannot model them properly. Is it possible in
> Phenix to define these two conformations as non-clashing and non-repulsive?
> Thank you, best regards, Sozanne Solmaz.
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