coreCIF items for final approval
David Brown idbrown at mcmaster.caTue Aug 7 16:33:23 BST 2007
- Previous message: coreCIF items for final approval
- Next message: coreCIF items for final approval
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://scripts.iucr.org/pipermail/coredmg/attachments/20070807/498ef4d2/attachment.html -------------- next part -------------- A non-text attachment was scrubbed... Name: idbrown.vcf Type: text/x-vcard Size: 298 bytes Desc: not available Url : http://scripts.iucr.org/pipermail/coredmg/attachments/20070807/498ef4d2/attachment.vcf
- Previous message: coreCIF items for final approval
- Next message: coreCIF items for final approval
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
More information about the coreDMG mailing list