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Core CIF dictionary in DDLm

  • To: Distribution list of the IUCr COMCIFS Core Dictionary Maintenance Group <coredmg@iucr.org>
  • Subject: Core CIF dictionary in DDLm
  • From: James Hester <jamesrhester@gmail.com>
  • Date: Tue, 12 Apr 2016 00:30:42 +1000
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Dear Core CIF Dictionary Management Group,

Many of you will be aware that COMCIFS decided at the Montreal meeting to move all IUCr-maintained DDL1 dictionaries to the new DDLm standard. The core CIF dictionary, as the basis upon which most other dictionaries are expressed, is the first in line to be approved. I would therefore like you to look over the attached draft core CIF DDLm dictionary and raise any issues in this mailing list.  You may find the short introduction to reading DDLm dictionaries at http://www.iucr.org/resources/cif/ddl/ddlm/docs/intro helpful, and the full set of DDLm attributes is provided in the latest ddl.dic file at ftp://ftp.iucr.org/pub/cifdics/DDLm_3.11.09.dic (itself a small DDLm dictionary). I have also provided a short overview of the DDLm core CIF dictionary below. Note that the dictionary makes use of the definition templates and default data found in the auxiliary dictionaries templ_enum.dic and templ_attr.dic (also attached). 

I propose a minimum 6 week discussion period (starting today) with any significant changes that have been accepted by the active members of this group automatically initiating a further 6 week wait from the date of the proposed change before being considered approved. Following approval by this group, the dictionary will be forwarded to COMCIFS for a formal approval.  It would of course be desirable for members of this group to positively indicate approval rather than remain silent. I note that the dictionary is large (over 1000 definitions) so I suggest that those of you who lack the time or expertise to review the whole dictionary review as many categories as you can deal with and indicate to us that you are commenting only on those particular categories.

It would be particularly helpful if you were to start a separate email thread for every significant issue. This makes it easier for those who come later to follow our discussion.

best wishes,
James Hester (acting Core CIF DMG chair)

DDL Core CIF dictionary overview


This draft DDLm core CIF dictionary was originally drafted by the Perth group, led by Syd Hall, and has been lightly edited by James Hester to bring it into line with the new CIF2 syntax and updates to the DDLm standard.

Major differences from DDL1

(1) Recommended datanames (the _definition.id attribute) are in <category>.<object> notation (i.e. contain a dot). The previous DDL1 datanames are still valid and are listed using the _alias tags. Where possible the recommended datanames should match their equivalents from the mmCIF dictionary (which are also in <category>.<object> notation.
(2) The dictionary makes use of the DDLm import mechanism to remove repetitive material from the dictionary proper into auxiliary files (templ_enum and templ_attr)
(3) Datanames may now be of vector or matrix type. So e.g. U_ij can be defined using a single dataname _atom_site_aniso.matrix_U
(4) The mathematical relationships connecting datanames are expressed using dREL methods. It is therefore possible to calculate F_calc using dictionary-aware software (e.g. look at the method for _refln.F_complex). These methods have been extensively tested by myself and the Perth group. If you are happy working with Python, the latest version of the PyCIFRW software fully understands these methods and can be used to test them.
(4a) The templ_enum dictionary contains all of the data required to perform the F_calc calculation, including all of the form factor coefficients and neutron scattering lengths.
(4b) Some new datanames have been created to record intermediate values in such calculation chains.
(5) DDLm 'nested' categories have been used to create 'splittable' loops. For example, atom_site_aniso is a category nested inside atom_site. This means that the anisotropic displacement parameters may either be listed separately, or together with the atom sites.
(6) Every loop category always has a single dataname that acts as a key.

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