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CIF description of twinning

  • To: Multiple recipients of list <coredmg@iucr.org>
  • Subject: CIF description of twinning
  • From: Brian McMahon <bm@iucr.org>
  • Date: Wed, 9 May 2001 10:44:00 +0100 (BST)
Dear Colleagues

I am sending this mailing to two discussion lists: the CIF Core dictionary
management group, and the structural chemistry list recently established
by Judy Flippen-Anderson. There has been some discussion recently among
structural chemists that it is rather difficult to extract information about 
(or even identification of) twinned crystal structures, for example from the 
Cambridge Structural database. One way of addressing this is of course to
have community standard ways of describing twinning in database entries.
Judy plans to canvass the strchem members for their views on what is needed.

I recalled our earlier discussions on twinning in the coreDMG which prompted 
the proposal of the following definitions, and so I offer them (a) as a
catalyst for the strchem discussion and (b) as a reminder of unfinished
coreDMG business (this is the third of my promised topics for extending the
Core dictionary to version 2.3).

The listing here incorporates Gotzon's initial proposals and Howard's
response. Readers new to the discussion will find the complete discussion
with carefully argued rationale at

I would suggest we proceed by inviting the strchem list to discuss their
perceived requirements for a while (in general terms rather than proposing
CIF definitions as such). I shall monitor the strchem discussion and bring
back any discussion to the coredmg list for consideration in a subsequent
review of these CIF names.

The proposed definitions are:

    _name                   '_diffrn_reflns_twin_id'
    _category                diffrn_reflns
    _type                    char
    _list                    yes
    _list_link_child         '_refine_ls_twin_id'
;              A unique identifier for each domain state whose presence
               is assumed to be permissible.

    loop_ _name              '_diffrn_reflns_twin_matrix_11'
    _category                diffrn_reflns
    _type                    numb
    _list                    yes
    _list_reference          '_diffrn_reflns_twin_id'
;              The set of twin-law matrices in which the ith matrix transforms
               the Miller indices of a reflection in the first domain state
               into those of the twin-equivalent reflection resulting from
               the ith domain state. A twin law transformation of Miller
               indices is written in matrix form as:

                       (h~i~)   (m~11~ m~12~ m~13~) (h~1~)
                       (k~i~) = (m~21~ m~22~ m~23~) (h~2~)
                       (l~i~)   (m~31~ m~32~ m~33~) (h~3~)

               The twin matrices are referred to the basis reciprocal to
               that derived from _cell_length_ and _cell_angle_. It is
               mandatory to specify all twin-law matrices, including that
               of the identity.

    _name                   '_refine_ls_twin_id'
    _category                refine
    _type                    char
    _list                    yes
    _list_link_parent        '_diffrn_reflns_twin_id'
;              The identifier of one domain state. This must be
               identical to a  _diffrn_reflns_twin_id.

    _category                refine
    _type                    numb
    _type_conditions         esd
    _list                    yes
    _list_reference          'refine_ls_twin_id'
    _enumeration_range       0.0:1.0
;              The refined values of the twin fractions. Twin fractions, k(i),
               are defined through the following expression:

                  G~c~=s^2^ Sumi k(i)|F|^2^~c,i~    (i=1,n)

                  Sumi k(i) = 1    (i=1,n)
               where G~c~ is the calculated twinned intensity for reflection
               h1 h2 h3, F~c,i~ the calculated structure factor of domain
               state i, s the overall scale factor and n the number of domain
               states. It is mandatory to specify the refined twin fractions
               of all domain states.

               The _enumeration_range of 0.0:1.0 is correctly interpreted as
               meaning (0.0 - 3u) =< x =< (1.0 + 3u).

    _name               '_refine_diff_twin_F_obs_deconvolution_description'
    _category                refine
    _type                    char
;              A description of the method used to calculate the
               Fourier coefficients used in electron density calculations.



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