School of EPS: Current Staff & Students

EPS Current Students and Staff

How to calculate the dummy atom position(s) for a nido Carborane Cage.



  1. Calculate the coordinates of the centroids X1A and X1B
    using CENT/X ATOM NAMES. For X1 these are (X, Y, Z)

  2. Calculate the unit vector from B(1) to X1A :- given as (x, y, z)
    (NB this is in fractions of unit cell length, and not Angstroms)
    by typing LINE X1A B1

  3. Convert the unit vector to Angstroms: (x/a, y/b, z/c)
    where a, b, and c are the unit cell lengths.

  4. Obtain the distance d1 by typing JOIN B1 X1B and then BANG X1B

  5. The coordinates of the dummy atom position D are given by :
    (assuming that d1 = d1')

               (X+d1*x/a, Y+d1*y/b, Z+d1*z/c)

  6. Finally, put the dummy atom in your *.ins file as:

    AFIX 1
    B12X 3   x  y  z  10.0000  10.0000
    AFIX 0

    i.e. having fixed zero occupancy and temperature factors. Put in HFIX as for closo structures but not including the dummy atom of course!

Please contact Dr Georgina Rosair for further information.

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