[phenixbb] Dual conformation on symmetry axis

Pavel Afonine pafonine at lbl.gov
Thu Feb 4 13:49:30 PST 2016

Hi Jan,

> An Arg side chain is located very close to a crystallographic 2-fold. 
> There is good evidence that the side chain has two conformations. 
> However, because of the 2-fold, conformer A overlaps with its symmetry 
> mate A*, as does conformer B. Phenix wants to avoid this 'clash' and 
> moves A and A* out of the density, same for B and B*.
> Is there a way to avoid this without reducing the symmetry? In the 
> real crystal, of course the two side chains are agnostic as to if they 
> are called A or B and will avoid one another ...

you can exclude involved residue from repulsion by using this parameter:

custom_nonbonded_symmetry_exclusions="chain A and resseq 123 and (altloc 
A or altloc B)"

You can do this in the GUI too by using search parameters option.

Let me know if it doesn't do it and I will think of an alternative solution.


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