Re: Allow default values for site symmetry in the geometry categories?
- To: "james.r.hester@gmail.com" <james.r.hester@gmail.com>, Distribution listof the IUCr COMCIFS Core Dictionary Maintenance Group <coredmg@iucr.org>
- Subject: Re: Allow default values for site symmetry in the geometry categories?
- From: "Spek, A.L. \(Ton\) via coreDMG" <coredmg@iucr.org>
- Date: Tue, 4 Apr 2023 08:25:23 +0000
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Sounds o.k. Ton Van:
coreDMG <coredmg-bounces@iucr.org> namens James H via coreDMG <coredmg@iucr.org> Dear Core DMG, We have adopted as a rule of thumb that we do not provide default values for data names when defining them in the dictionary. This is justified on the grounds that a missing value doesn't mean that the most
likely value should be substituted, as the programmer may simply have not output that data name. So, for example, if the temperature is missing, that doesn't mean room temperature. This blanket rule included the GEOM categories, which are used to describe bonds and angles. Each atom participating in the bond/angle is identified by providing the "site symmetry": which means in this case
the symmetry operation and cell translation that should be applied to the asymmetric unit coordinates. If the atom in the bond just has its asymmetric unit position, the site symmetry would be "1_555". A request has come through to make this the explicit default
site symmetry, that is, if no site symmetry is supplied then it is assumed to be "1_555". The justification for allowing an explicit default in this case is that an error is easily detectable, as the GEOM categories can be reconstructed from the supplied
atomic sites. In this way it is qualitatively different from the temperature example above, where there is no way of recovering the true value. Some further practical benefits of the request are outlined in
https://github.com/COMCIFS/cif_core/issues/362#issue-1652795179. If this group has no objections to the above proposal, I further suggest we adopt a general principle that default values can be provided in the dictionaries if an error can be detected by derivation from
values that are known to be present. In this case, as the GEOM categories explicitly refer to the contents of both ATOM_SITE and SPACE_GROUP(_SYMOP), the values from which the bonds and angles are calculated should be present. Please comment. all the best, James.
T +61 (02) 9717 9907 |
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