Discussion List Archives

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: Ambiguity in atom_site.disorder_group value -1

  • To: "coredmg@iucr.org" <coredmg@iucr.org>
  • Subject: Re: Ambiguity in atom_site.disorder_group value -1
  • From: "Bollinger, John C via coreDMG" <coredmg@iucr.org>
  • Date: Mon, 17 Oct 2022 22:18:12 +0000
  • Accept-Language: en-US
  • ARC-Authentication-Results: i=1; mx.microsoft.com 1; spf=passsmtp.mailfrom=stjude.org; dmarc=pass action=none header.from=stjude.org;dkim=pass header.d=stjude.org; arc=none
  • ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=microsoft.com; s=arcselector9901;h=From:Date:Subject:Message-ID:Content-Type:MIME-Version:X-MS-Exchange-AntiSpam-MessageData-ChunkCount:X-MS-Exchange-AntiSpam-MessageData-0:X-MS-Exchange-AntiSpam-MessageData-1;bh=XFhjXdDT6i13X/qS0BqN2W+sVakQ+Qi1Ch11GNbrMi4=;b=OeXNA6CslIIWcUm2rafMoN+b8atcTqjnXNeGWyXWF4um/TfP0IMXRIahvH5ifBUKgmrm2OUdkQh6G5YKXNKWio8k1CZMsDbiem3kfibnFET/J/0d9bURTmcvUkmWd3/3if/P9t4mTkgtgAJXYFrB/Sm+USd7+xmchO+LuxF1F7ApZV2G+nvI7b0/eva5/FhRCLabZ3yeeuelcwTAW80n26si7pPERslU9NDBc754rqPfbkvV7a4nWDEPD7Ug8R349VMujhaMjH1FR2YPXslQA8pK+1y9OeCEVxhFR4c+KKeWeuGqTOti6eAr7/2j/ZfLsDgjXqk4gOZrH+aIsVpEBQ==
  • ARC-Seal: i=1; a=rsa-sha256; s=arcselector9901; d=microsoft.com; cv=none;b=RRfTj6cOuLSOer7bLexn0SRRhGxRxU/pDvaR2jePDW8skiJUss/tLQlDlH5HbTfdcWr4o7YX286mAxb4I8kPkPh/X3dZjmDfP4jw2PhZijvTlauZsuWFeRV5PpcRGzdSqkgL97f/gsZuV9FEwT6DcaS1TpHhfb31QRu4kRmpiXVfuapazFpiluYDHpM3KvywHEHsBIp362+4Z/Tpl12KdO1mujUmpQ3ego7F70Eqb34FJheNa9rNakkY8xURw4O5WZ9ME8T1Gd5XL9EKhB9WYe3hwA0pJPAgOn8gPpQ2Sffdfv2D7b1DL64AJp8WcbXwmyp6pO7oUzQQuCjPbP+Ybw==
  • Cc: "Bollinger, John C" <John.Bollinger@STJUDE.ORG>
  • In-Reply-To: <CAF_YUvVJnqehHZLR6pML=UA-n1j4oAmABciUhB4Ek9R+G+G7QA@mail.gmail.com>
  • References: <CAF_YUvVJnqehHZLR6pML=UA-n1j4oAmABciUhB4Ek9R+G+G7QA@mail.gmail.com>
Hi Bob,

Yes, when a moiety is disordered about a symmetry element with multiplicity 2, such as a 2-fold rotation axis, there will be half as many per unit cell as there would ordinarily be for a moiety at a general position of the space group -- much the same as if it were ordered (and therefore symmetric) around the symmetry element.  Analogous applies for disorder around higher-symmetry positions.

I believe the specific semantics of negative disorder group numbers is drawn from the SHELX system.  In computing the connection list for an atom with a negative disorder group number, SHELX considers only the given coordinates of other atoms, if any, in that group, plus all symmetry copies of atoms belonging to group 0.  That is, symmetry copies of other atoms in the same group are not considered, unlike for disorder groups with positive numbers.

I'm afraid I'm not happy with the suggested revision.  I would prefer to see the original definition augmented rather than replaced, because "disordered about a special position" is precise and meaningful to me, even though I acknowledge that its meaning may be less clear to some.  Perhaps something like this would be a suitable improvement:

====
[...] Sites belonging to the same group are simultaneously occupied, but those belonging to different groups are not.

(paragraph break)

A minus prefix (e.g. '-1') is used to indicate that the group is disordered about one or more symmetry elements. In addition to not being occupied simultaneously with sites belonging to different groups, the sites of such a group also are not occupied simultaneously with symmetry equivalents of sites belonging to the same group.  That is, the group's symmetry equivalents are among its disorder complements.
====

Notes:

 - "disordered about one or more symmetry elements" is both more accurate than "disordered about a [singular] special position" and probably easier to understand for the casual crystallographer.

 - I prefer to stick to defining the term, as opposed to specifying how software should behave in light of the definition.  We cannot anticipate all uses of CIF data, but we can hope that if our definitions are clear enough then they will equip programmers to decide for themselves how best to use CIF data for their particular purposes.

Best regards,

John

--
John C. Bollinger, Ph.D., RHCSA
Computing and X-ray Scientist
Department of Structural Biology
St. Jude Children's Research Hospital
From: coreDMG <coredmg-bounces@iucr.org> on behalf of Robert Hanson via coreDMG <coredmg@iucr.org>
Sent: Monday, October 17, 2022 2:38 PM
To: coredmg@iucr.org <coredmg@iucr.org>
Cc: Robert Hanson <hansonr@stolaf.edu>
Subject: Ambiguity in atom_site.disorder_group value -1
 
Caution: External Sender. Do not open unless you know the content is safe.

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.


Email Disclaimer: www.stjude.org/emaildisclaimer
Consultation Disclaimer: www.stjude.org/consultationdisclaimer
 
_______________________________________________
coreDMG mailing list
coreDMG@iucr.org
http://mailman.iucr.org/cgi-bin/mailman/listinfo/coredmg

[Send comment to list secretary]
[Reply to list (subscribers only)]