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Ambiguity in atom_site.disorder_group value -1

  • To: coredmg@iucr.org
  • Subject: Ambiguity in atom_site.disorder_group value -1
  • From: Robert Hanson via coreDMG <coredmg@iucr.org>
  • Date: Mon, 17 Oct 2022 14:38:13 -0500
  • Cc: Robert Hanson <hansonr@stolaf.edu>
Hello! It has been suggested that I address this issue with this austere group. The issue is that specifying -1 for atom_site.disorder_group has some perhaps unintended consequences.


The comment we have is this:

A minus prefix (e.g. '-1') is used to indicate sites disordered about a special position.

Brian McMahon helped me understand what that is about. Basically, as I understand it now, sometimes disorder groups are based on space group symmetry. When that happens, rather than using two sets (say) of general positions to describe two different but related disordered groups, only one general position set is required -- applying symmetry then generates the others. Thus, we don't need "group 1" and "group 2"; we only need "group -1".

Visualization software such as Mercury or Jmol should recognize this and refrain from connecting atoms that are in different symmetry-related groups (using whatever distance-related algorithms they have for that). Recently,  though,  I was working with a CIF file with such a designation (see "disorder-1.cif", attached) and realized that Jmol was handling these incorrectly. I fixed that in Jmol 14.32.77 but also noticed that Mercury 2022.2.0 also had the same issue -- it is connecting atoms across symmetry-related sets:


image.png

That fixed for Jmol, I realized another issue that is a bit curious. The important question now for me is how the n copies of the symmetry-equivalent groups are related in a space group with n symmetry operators. For example, in this case, seven "ghosts" are created by applying all 8 operators in the example I provided.

disorder-1.png
Is it expected (I think it is) that four copies of the structure are present simultaneously in the actual crystal? It's just that within each pair we might not know which is present? It's this pairing aspect that seems to be missing -- if I have the idea right. Certainly the business about being "about a special position" implies that there is a special operator, perhaps a C2 axis or an inversion center, that is considered a key operator. But this is not described in the CIF dictionary description.

Brian mentioned that I should offer a change in the description. Here is my suggestion:

A minus prefix (e.g. '-1') is used to indicate that related disordered groups are symmetry equivalent
   (for example, involving two orientations related by a C2 axis or an inversion center) and thus
   are not listed individually in the atom_site block. In this case, software generating structures
   should consider symmetry-equivalent groups derived from these sites to be separately bonded
   entities.

As for rendering, I suggest that Mercury has a bug there in terms of bonding. Also with its rendering of the asymmetric unit, which for some reason is using the wrong coordinate for the chlorine atom:
image.png

As for Jmol, it is doing this correctly. But in order to do that, it has to create eight independent "alternative locations"

$ print {*}.altloc.pivot
{
  ""  :  6
  "1"  :  11
  "A"  :  11
  "B"  :  11
  "C"  :  11
  "D"  :  11
  "E"  :  11
  "F"  :  11
  "G"  :  11
 }

Which, of course, is a bit odd.

Comments?

Bob




--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

We stand on the homelands of the Wahpekute Band of the Dakota Nation. We honor with gratitude the people who have stewarded the land throughout the generations and their ongoing contributions to this region. We acknowledge the ongoing injustices that we have committed against the Dakota Nation, and we wish to interrupt this legacy, beginning with acts of healing and honest storytelling about this place.

disorder-1.cif

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