coreCIF items for final approval

David Brown idbrown at mcmaster.ca
Tue Aug 7 16:33:23 BST 2007


Dear Howard,

No, you seem to have mistaken the meaning of _geom__bond_multiplicity.  
It refers just to the environment of the first named atom as it appears 
in the bond list.  The environement of the first atom can be expressed 
in two possible ways, either by listing only the symmetry unique bond 
lengths and using the multiplicity to generate the additional bonds (of 
course this would not generate the site_symmetry code for the second 
atom but his would not be of interest if this mode were used).  In the 
second mode all the bonds around the first named atom would be listed in 
which case the multiplicty would not be needed.  Setting the default 
value to 1.0 allows software to treat all geom_bond lists the same way, 
by using the multiplicity to generate the additional symmetry-related bonds.

Howard Flack wrote:

>>The only place where you propose a definitive change is in item 8 and I accept this change.  The only alteration I would make to your propsed wording is to replace 'the same appropriate multiplicity' with 'a multiplicity of 1' which is in any case the default value.
>>
>
>   I think I do not agree with your revised wording.  To make clear what 
>I have in mind, here is your example of a full bond list according to 
>the way that I think it should be done.  The text should correspond to 
>this example.
>
>;
>'An example where the multiplicity is given with a full bond list'
>;
>loop_
>_geom_bond_atom_site_label_1
>_geom_bond_atom_site_label_2
>_geom_bond_site_symmetry_2
>_geom_bond_distance
>_geom_bond_multiplicity
>Ca1   F1   1_555  2.495(9)    1
>Ca1   F2   1_555  2.291(10)   2
>Ca1   F2   2_555  2.291(10)   2
>Ca1   F2   3_565  2.391(11)   2
>Ca1   F2   4_555  2.391(11)   2
>Ca1   F3   2_545  2.214(11)   2
>Ca1   F3   5_555  2.214(11)   2
>Cr1   F1   1_555  1.940(11)   2
>Cr1   F1   2_555  1.940(11)   2
>Cr1   F2   1_555  1.918(9)    2
>Cr1   F2   2_555  1.918(9)    2
>Cr1   F3   1_555  1.848(10)   2
>Cr1   F3   2_555  1.848(10)   2
>;
>

What you have written, Howard, in the above example would generate 13 
bonds around Ca1 and 12 bonds around Cr1 rather than the correct numbers 
of 7 and 6 respectively.  In this case all the bonds around Ca1 and Cr1 
are listed explicitly so the mulptiplicities are all 1.

I have rewritten the _definition in order to make this point clearer.  
The revised dictionary text is as follows:

data_geom_bond_multiplicity
    _name               '_geom_bond_multiplicity'
    _category            geom_bond       
    _type                numb       
    _list                yes       
    _list_reference      '_geom_bond_atom_site_label_'   
    _enumeration_range   0:
    _enumeration_default 1
    _definition
;       The number of times the given bond appears in the environment of
        the atoms labelled _geom_bond_atom_site_label_1. 
        This item is used in cases where only the unique set of symmetry
        independent bonds are listed.  The multiplicity then allows all
        the symmetry-related bond lengths in the environment of the first
        atom to be generated. 
        In cases where all the bonds in the environment of the first atom
        are listed explicitly, the multiplicity of each of the bonds would
        have the default value of 1.
;

loop_
_example_detail
_example
'An example showing a listing of only the symmetry unique bonds'
;
loop_
_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_geom_bond_distance
_geom_bond_multiplicity
Ca1   F1   2.495(9)    1
Ca1   F2   2.291(10)   2
Ca1   F2   2.391(11)   2
Ca1   F3   2.214(11)   2
Cr1   F1   1.940(11)   2
Cr1   F2   1.918(9)    2
Cr1   F3   1.848(10)   2
;
'An example where the multiplicity is given with a full bond list'
;
loop_
_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_geom_bond_site_symmetry_2
_geom_bond_distance
_geom_bond_multiplicity
Ca1   F1   1_555  2.495(9)    1
Ca1   F2   1_555  2.291(10)   1
Ca1   F2   2_555  2.291(10)   1
Ca1   F2   3_565  2.391(11)   1
Ca1   F2   4_555  2.391(11)   1
Ca1   F3   2_545  2.214(11)   1
Ca1   F3   5_555  2.214(11)   1
Cr1   F1   1_555  1.940(11)   1
Cr1   F1   2_555  1.940(11)   1
Cr1   F2   1_555  1.918(9)    1
Cr1   F2   2_555  1.918(9)    1
Cr1   F3   1_555  1.848(10)   1
Cr1   F3   2_555  1.848(10)   1

;
Of course the _multiplicity could be omitted in the second example and 
usually would be.  In fact the second example itself could be omitted as 
being trivial and not illustrating the way one would normally construct 
the CIF.  Note that in the first example no site symmetries are given 
for the F atoms, since in this case the author is only interested in the 
bond lengths but needs to know which, if any are duplicated by 
symmetry.  In the seocnd example we expect to find the site_symmetry 
codes since all the symmetry related bonds are listed.


David
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