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--}
CONStraints
INTERaction ( not ( store1 ) ) ( all )
weights * 1. end
INTERACTIOn ( store1 ) ( all )
weights * 1. pvdw 0. pele 0. end
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 ;-)
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