Re: [ccp4bb] Symmetry operator
I am afraid now I just use PISA at the EBI to answer this sort of question . It tells you the answer with lots of other useful information as well, and then you can use your intelligence to see why that operator is the correct one! Eleanor On 11 Jan 2013, at 01:05, 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
Re: [ccp4bb] Symmetry operator
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
Re: [ccp4bb] Symmetry operator
coot: show symmetry molecules, then save symmetry molecule and you have your tetramer most likely Jürgen On Jan 10, 2013, at 7:48 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 .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
Re: [ccp4bb] Symmetry operator
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
