SO4 in a special position (deja vu ?)

Gerard 'CD' Kleywegt GERARD at XRAY.BMC.UU.SE
Thu Jun 15 16:43:39 EST 1995

Isn't it time for an X-PLOR FAQ ?  A very similar
question was asked & answered sometime in
November last year.  Here goes again, now for a
three-fold axis:

Use only an SO2 unit; position the sulphur and one
oxygen *exactly* on the threefold and let the other
oxygen point into one of the asymmetric units.

two other important points:

(1) the coordinates of the atoms that lie exactly on the
    three-fold must be very precise in order for X-PLOR to
    recognize them as being in a special position
    (I had a three-fold in P2(1)3 & figured out an
    equation for this; then calculate two points on
    the line, read them into O as if they were a
    molecule and draw a bond between them; then 
    move_atom your special atoms so they lie more
    or less exactly on the axis - and inside the
    difference density obviously ;-)

(2) do not reduce occupancies for the atoms in special
    positions; X-PLOR does that for you

finally, you have to exclude interactions with atoms
in special positions, for instance by using:

vector ident (store1) ( resi 900 ) {assuming residue #900}
                                   {is your special SO4--}
   INTERaction ( not ( store1 ) ) ( all )
       weights * 1. end
   INTERACTIOn ( store1 ) ( all )
       weights * 1. pvdw 0. pele 0. end

to avoid listings of "bad contacts" between the
sulphate atoms use:

parameter nbonds wmin=0.1 end

--gerard kleywegt
  bmc, uppsala

ps:- i didn't think of all this myself, obviously;
     Axel told me this when I encountered a PO4
     on a xtall. three-fold ;-)

More information about the X-plor mailing list