On Thu, Sep 6, 2012 at 12:21 PM, Dave Lodowski
Dear all, I am attempting to add a bond restraint that connects a serine in one molecule to a carbon located in its symmetry mate in the adjacent unit cell.
Atom selection 1: chain 'A' and resid ' 230 ' and name ' C ' and altloc 'A' Atom selection 2: chain 'A' and resid ' 179 ' and name ' OG ' and altloc 'A' and (*insert symmetry keyword here*) 'x-1,y,z' (altloc B in both cases is not covalently attached)
I cannot seem to find a complete description of the atom selection syntax in the Phenix documentation to specify which symmetry mate. and the gui/ phenix graphics does not have any way to generate symmetry mates.
No, but the GUI does have an interface to input the symmetry operator for custom bonds - if you click the "custom geometry restraints" button on the "Refinement settings" tab, you get an interface that looks like the attached image. Select a bond and click the "Other options" button, and it will open a menu that includes an option to specify the symop. The selection syntax itself doesn't handle symmetry operators; it's a separate parameter (symmetry_operator) for the bond definition (the other restraints don't support symops yet). Details are here: https://www.phenix-online.org/version_docs/dev-1150/refinement.htm#anch344 -Nat