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Re: CIF description of twinning



Dear Brian,

Many thanks for your CIF proposals. I will have a good look at them, but
I doubt if I will be able to get back to you for about three weeks
because I am going to two meetings in the US and must deal with a lot of
administrative chores before I go. I am very grateful that you are
giving me early warning, you have to bear in mind that even when I
release a new version of my programs (which I do at about 5 year
intervals) it takes two or three years to persuade most of the the 2000+
groups using them to upgrade.

Best wishes, George

=========================================================================
Brian McMahon wrote:
> 
> 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
>     http://www.iucr.org/iucr-top/lists/coredmg/msg00123.html
>     http://www.iucr.org/iucr-top/lists/coredmg/msg00143.html
>     http://www.iucr.org/iucr-top/lists/coredmg/msg00146.html
> 
> 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:
> 
> ===============================================================================
> data_diffrn_reflns_twin_id
>     _name                   '_diffrn_reflns_twin_id'
>     _category                diffrn_reflns
>     _type                    char
>     _list                    yes
>     _list_link_child         '_refine_ls_twin_id'
>     _definition
> ;              A unique identifier for each domain state whose presence
>                is assumed to be permissible.
> ;
> 
> data_diffrn_reflns_twin_matrix_
>     loop_ _name              '_diffrn_reflns_twin_matrix_11'
>                              '_diffrn_reflns_twin_matrix_12'
>                              '_diffrn_reflns_twin_matrix_13'
>                              '_diffrn_reflns_twin_matrix_21'
>                              '_diffrn_reflns_twin_matrix_22'
>                              '_diffrn_reflns_twin_matrix_23'
>                              '_diffrn_reflns_twin_matrix_31'
>                              '_diffrn_reflns_twin_matrix_32'
>                              '_diffrn_reflns_twin_matrix_33'
>     _category                diffrn_reflns
>     _type                    numb
>     _list                    yes
>     _list_reference          '_diffrn_reflns_twin_id'
>     _definition
> ;              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.
> ;
> 
> data_refine_ls_twin_id
>     _name                   '_refine_ls_twin_id'
>     _category                refine
>     _type                    char
>     _list                    yes
>     _list_link_parent        '_diffrn_reflns_twin_id'
>     _definition
> ;              The identifier of one domain state. This must be
>                identical to a  _diffrn_reflns_twin_id.
> ;
> 
> data_refine_ls_twin_fraction
>     _category                refine
>     _type                    numb
>     _type_conditions         esd
>     _list                    yes
>     _list_reference          'refine_ls_twin_id'
>     _enumeration_range       0.0:1.0
>     _definition
> ;              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).
> ;
> 
> data_refine_diff_twin_F_obs_deconvolution_description
>     _name               '_refine_diff_twin_F_obs_deconvolution_description'
>     _category                refine
>     _type                    char
>     _definition
> ;              A description of the method used to calculate the
>                Fourier coefficients used in electron density calculations.
> ;
> 
> ===============================================================================
> 
> Regards
> Brian

-- 
Prof. George M. Sheldrick
Dept. Structural Chemistry
Tammannstr. 4
D37077 Goettingen, Germany
Tel. +49-551-393021
Fax. +49-551-392582

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