[phenixbb] restraining covalent links between symmetry related molecules

Nathaniel Echols nechols at lbl.gov
Thu Sep 6 13:17:50 PDT 2012

On Thu, Sep 6, 2012 at 12:21 PM, Dave Lodowski <lodowski at gmail.com> wrote:
> 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:



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