I need to amend that and make a couple of corrections, after thinking about it.
First, the rotation-translations shouldn't be sensitive to the origin. Second,
if it has C4 ("square") symmetry, then you only need one generator
(rotation-translation) to make the tetramer, and the two monomers should be
adjacent.
If it is T4 ("tetrahedral") symmetry, then you need two generators, with one
generator made from a pair of monomers opposite and one generator made from a
pair adjacent.
James
On Jan 10, 2013, at 6:05 PM, James Stroud wrote:
> The transformation matrix describing the symmetry is sensitive to the
> coordinate system origin. You should center the entire tetramer on the origin
> (0, 0, 0), where the origin coincides with the point symmetry element. If
> you have a tetramer with true point symmetry, then the center of the tetramer
> should be the center of mass. Then you can use lsq-expl from O or whatever
> the equivalent is in pymol, phenix, or coot to get the transformation matrix
> between any two monomers.
>
> Repeated application of that transformation matrix to any monomer of the
> tetramer should generate the tetramer.
>
> James
>
> On Jan 10, 2013, at 5:48 PM, james09 pruza wrote:
>
>> Hi,
>>
>> Which program outputs the symmetry operator (rotation and translation)? I
>> have a dimer in the asymmetric unit and need to know the symmetry operator
>> to get a tetramer, the active molecule.
>> James
>>
>
