Ambiguity in atom_site.disorder_group value -1

[Robert Hanson]

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.

https://www.iucr.org/__data/iucr/cifdic_html/2/cif_mm.dic/Iatom_site.disorder_group.html

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
<https://sourceforge.net/projects/jmol/files/> but also noticed that
Mercury 2022.2.0 also had the same issue -- it is connecting atoms across
symmetry-related sets:


[image: 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.

[image: 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: 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.*
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.iucr.org/pipermail/coredmg/attachments/20221017/6928f331/attachment-0001.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: disorder-1.png
Type: image/png
Size: 64304 bytes
Desc: not available
URL: <http://mailman.iucr.org/pipermail/coredmg/attachments/20221017/6928f331/attachment-0003.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 353682 bytes
Desc: not available
URL: <http://mailman.iucr.org/pipermail/coredmg/attachments/20221017/6928f331/attachment-0004.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 189501 bytes
Desc: not available
URL: <http://mailman.iucr.org/pipermail/coredmg/attachments/20221017/6928f331/attachment-0005.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: disorder-1.cif
Type: application/octet-stream
Size: 1933 bytes
Desc: not available
URL: <http://mailman.iucr.org/pipermail/coredmg/attachments/20221017/6928f331/attachment-0001.obj>