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 \ / M / \ 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 symmetry_operation=-x,y,-z (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. Ralf