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Re: [ddlm-group] Your thoughts on correct approach for DDLmmodulated structures dictionary GEOM categories

  • To: ddlm-group <ddlm-group@iucr.org>
  • Subject: Re: [ddlm-group] Your thoughts on correct approach for DDLmmodulated structures dictionary GEOM categories
  • From: James Hester <jamesrhester@gmail.com>
  • Date: Fri, 7 Apr 2017 15:25:19 +1000
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For the benefit of those reading this thread in the future, this problem has been resolved by using the new _audit.formalism dataname to signal redefinition of datanames and categories.

On 17 November 2016 at 16:57, James Hester <jamesrhester@gmail.com> wrote:
Dear DDLm-group,

I am currently going through the DDLm conversion of the modulated structures dictionary. It goes without saying that it will be split into a core_cif compatible section and an _audit.schema-using extension dictionary, as numerous categories receive extra keys due to the extra m1,m2,m3... reflection indices. That in itself is not a problem; however, I have come across the following "interesting" situation in the GEOM categories, and would like your input into how to resolve this:

The core cif method of identifying a particular atom site for geometry calculation uses the atom label and a symmetry operator of the form n_qrs, where n is a symmetry operator and qrs are unit cell translations + 5.  So the key datanames for the list of bonds (GEOM_BOND category) are atom_labels 1 and 2, and site_symmetry 1 and 2.  The bond length can be calculated using the information encoded in these keys.

The DDL1 modulated structures dictionary needs more than three translations, so defines new datanames site_ssg_symmetry 1,2 where the value might be n_qrstuv (i.e. more translations).  The intention is clearly to replace the original site_symmetry keys with the site_ssg_symmetry keys, so, strictly speaking, GEOM_BOND et. al. are new categories in the ms CIF dictionary. This is starkly evident in the dREL for geom_bond.distance from core_cif: it is no longer correct, reflecting the fact that most core cif compatible software that seeks to (re)calculate geom_bond.distance will fail when presented with a msCIF file.

We seek a resolution that keeps the dREL correct and minimises the chances of incorrect interpretation of a CIF file.

I see two alternatives:
(1) Allow dictionaries that operate under a different _audit.schema to replace keys, thereby keeping the same category name for what is essentially a different category. Any dREL-containing definitions must have the dREL rewritten or removed.

Advantages: "Very similar" datanames do not need to be renamed. DDLm datanames can match DDL1 datanames as closely as possible
Disadvantages: potential trivial redefinition of many datanames in all affected categories. Sets a precedent for giving different categories the same name?

(2) Change the GEOM_ categories to (e.g.) GEOM_SSG categories

Advantages: Strictly correct, no chance of confusion for _audit.schema non-aware programs (hopefully fewer of these as time goes on)
Disadvantages: Will proliferate datanames?

I am inclined towards (1) on the grounds that:
(a) Once _audit.schema is declared and checked, it is clear that the CIF software author is aware of MS CIF, including any redefinitions, so there is little danger of silent software mistakes;
(b) Fundamentally the site_symmetry_ datanames are decomposable into 4 key columns each (symmetry operator, 3 translations).  So MS CIF is simply adding more key columns, in accordance with how we expect _audit.schema to operate.
(c) We (COMCIFS) can always reserve the right to reject new dictionaries that attempt a category rename.

Can any of you see a problem with option (1)?


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T +61 (02) 9717 9907
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M +61 (04) 0249 4148
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