[phenixbb] ReadySet for special position metal

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Mon Apr 26 21:08:11 PDT 2010

Hi Tiancen,

> I am refining a structure with a metal ion on a 2-fold axis, coordinated by
> four histidines, two from the ASU and two from symmetry. I used
> phenix.ready_set to generate the metal coordination file and input it into
> phenix.refine. However, phenix.refine complains that the customized angle
> restraints contain a special position atom and cannot continue. I am using
> Phenix 1.5.2. Could anyone suggest me how to solve this problem?

It is still a limitation in the current release.
As a first step, just remove the angles. If the metal coordination
isn't sufficiently stable in refinement, you can add back the
angle restraints as pseudo bonds; symmetry bonds are fully supported.
If this is your situation

    A     B
     \   /
     /   \
    B'    A'

with A, B in the asymmetric unit and A', B' the symmetry-equivalents
due to the two-fold, define a custom bond between A and B,
and a second bond between A and B'. For the latter you need
to specify something like


(assuming the two-fold is parallel y) but most likely with
additional unit translations, e.g. -x+1,y,-z-1 . You can obtain
the exact symmetry opertion with Coot: ask it to draw symmetry
copies, then click on B' to have it tell you what symmetry operation
was used to draw it.


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