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RE: Ambiguity in atom_site.disorder_group value -1

Hi Bob,

 

You asked,

 

Q: Why did you choose the C2 axis rather than the Ci point, for example? Same disordering there, I think. Maybe the C2 is "more obvious"?

 

I eyeballed it from the images.  It appears that if you take any of the specific locations in the unit cell for the disordered CpMCl moiety, then it is a 2-fold rotation that relates the two overlapping conformations appearing at that location.  The axes for those particular rotations necessarily pass through the same area as the pairs of conformations they relate, which is the sense in which they are “local”.  Sure, each of those is also related by symmetry to other copies elsewhere in the structure, but for the purpose of the terminology, I’m looking only at overlapping pairs.  Because it’s the overlap that most characterizes the disorder in this case.

 

Locally meaning "involving a specific symmetry element of the crystallographer's choice"?

 

Locally meaning “relating the components of pairs of overlapping conformations”. I.e. the pairs containing atoms that are close enough that JMol would compute bonds between them if it didn’t know better.

 

John, would you agree that "symmetry equivalents" are based on symmetry operations? Maybe that's the problem -- You are identifying and building your description around symmetry elements, which are not the subject of a CIF file, rather than symmetry operations, which are all I have to go on in general when working with a CIF file.

 

I would agree that it is valid to view symmetry equivalents as being based on symmetry operations, but that is not my preferred characterization.  Symmetry operations in the form that they are expressed in core CIF are derivatives of symmetry elements and choice of origin.  They are not the fundamental concept.  For example, I can look at a packing diagram and say that it looks like there is a mirror plane here and an inversion center over there, and that these groups are related to each other by one and those by the other.  That doesn’t depend on functional forms for representing those symmetry relationships.

 

I am attempting to build a definition in terms of the most relevant domain concepts, using wording that I think is common in the field and / or likely to be understood by crystallographers.  This is the best way I know to write definitions.

 

Yes, I can decode a symmetry operation and see that it refers to a C2 axis. Yes, I can construct a C2 axis that relates pairs of clearly overlapping disordered group complements (terminology?). But in this case, the "local" C2 axis I think you are referring to is not one of the given CIF symmetry operations. That would actually be quite challenging to define just from the information in a CIF file, I think.

 

And I wouldn’t expect JMol to do that.  The most I would expect it to do is see that the disorder group was negative, and to respond by not computing bonds between the atom sites of different symmetry copies of that group (or of altogether different disorder groups).  Honestly, it puts JMol a step above that it pays special attention to rendering disordered groups at all.

 

I just have never heard of "local symmetry equivalents" -- that is completely new to me. But if that is what people say, OK.

 

I think other people *would* say that if they felt a need to draw attention to that particular distinction.  I’m just applying the word “local” in a conventional English sense to qualify “symmetry equivalents”.  But I think crystallographers would not typically think it necessary to elaborate on “disordered about a symmetry element” (or “about a special position”).  I submit the original definition as evidence.  That doesn’t mean that the definition should not be augmented, however.

 

That is, some of the group's symmetry equivalents are among its disorder complements.

 

Not sure this one is needed.

 

Funny.  That’s the one that I supposed would be the most meaningful.  Or at least the most clue-me-in-that-there’s-something-to-pay-attention-to.

 

 

John

 

 

From: Robert Hanson <hansonr@stolaf.edu>
Sent: Tuesday, October 18, 2022 1:04 PM
To: Distribution list of the IUCr COMCIFS Core Dictionary Maintenance Group <coredmg@iucr.org>
Cc: Bollinger, John C <John.Bollinger@STJUDE.ORG>
Subject: Re: Ambiguity in atom_site.disorder_group value -1

 

Caution: External Sender. Do not open unless you know the content is safe.

 

 

 

On Tue, Oct 18, 2022 at 11:42 AM Bollinger, John C via coreDMG <coredmg@iucr.org> wrote:

Hi Bob,

 

My thinking is that the crystallographer might recognize "a" special symmetry element, but the application of symmetry creates n copies, not two, in a space group with n symmetry operations. Right?

 

Thus, fundamentally, there is no such concept of a "specific" symmetry element. All n copies symmetry related, but all are not "complementary".

 

There seems to be some mismatching terminology going on here. When I say “a symmetry element”, I mean a mirror plane, axis of rotational symmetry, etc. -- that is, an element of the relevant space group -- as realized in the particular structure.  I was under the impression that this usage was pretty conventional.  Surely you’ve listened to many talks and read many articles that discuss how a crystal structure contains a mirror plane here, or an inversion center there, or a rotation axis wherever?  I know I have.

 

Certainly my understanding. We are talking about the same thing. I was reading "symmetry element" as you describe. My point was that there are also inversion centers, glide planes, and translations all at work in this example. Let's see what reads below...

 

 

 

In this sense, there are many symmetry elements in any crystal structure, and usually several distinct ones in or passing through each unit cell.  The International Tables present diagrams showing their types and locations.  So yes, in this sense there absolutely is a concept of a specific symmetry element.  But you seem to be using the term differently.

 

 

Don't think so.

 

This group can be considered to be disordered about any of these symmetry elements.

 

Yes and no.  As a matter of terminology, when I say a group is disordered about a symmetry element, I am employing the typical reduction of the overall structure to a crystallographically unique unit, and looking at the symmetry elements that relate the chosen unit to a symmetry equivalent that overlaps that particular unit in space.  I think that this, too, is a relatively common usage in chemical and crystallographic jargon.  When I allow for the possibility of a group being disordered about multiple symmetry elements, I am talking about cases where the disorder occurs at a site where multiple symmetry elements intersect.  At such a site, multiple elements may generate images of the same unique unit that all overlap the original unit.

 

Sure. Q: Why did you choose the C2 axis rather than the Ci point, for example? Same disordering there, I think. Maybe the C2 is "more obvious"?

 

 

It is also true that when there is disorder, one can (always) find symmetry elements, sometimes of different kinds, that generate overlaps with a chosen unique unit from distinct symmetry copies of that unit.  But that’s not what I’m talking about, and I don’t think it’s very interesting because it follows as a necessary consequence of translational symmetry.

 

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. 

 

I don't understand this statement. Why would it be true that sites related by symmetry are "not being occupied simultaneously"?

 

It took me embarrassingly long to work out what the problem was here.  Which is a great demonstration of why data dictionaries are valuable, and why collaborative development of them is important.  The point that is not adequately conveyed by my previous suggesting wording is that the bit about symmetry equivalents not being simultaneously occupied should be understood locally, not globally. 

 

Locally meaning "involving a specific symmetry element of the crystallographer's choice"?

 

 

Perhaps this refinement would be more acceptable:

 

====

[...] 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 atom sites of such a group are not occupied simultaneously with local symmetry equivalents of sites belonging to the same group.  That is, some of the group's symmetry equivalents are among its disorder complements.

 

Begs the question of what is "local". Should I know what that means?

 

John, would you agree that "symmetry equivalents" are based on symmetry operations? Maybe that's the problem -- You are identifying and building your description around symmetry elements, which are not the subject of a CIF file, rather than symmetry operations, which are all I have to go on in general when working with a CIF file.

 

Yes, I can decode a symmetry operation and see that it refers to a C2 axis. Yes, I can construct a C2 axis that relates pairs of clearly overlapping disordered group complements (terminology?). But in this case, the "local" C2 axis I think you are referring to is not one of the given CIF symmetry operations. That would actually be quite challenging to define just from the information in a CIF file, I think.

 

$ draw symop @2 @13
2 -x+1/2,y,-z+1 C2 axis

 

whereas the stated operation is:

 

 '-x+1/2, y, -z'

 

Minor detail there, but technically this is a different "C2 axis". It relates our asymmetric unit to a different copy. Maybe I should call this a "global" C2 axis? Not sure.

 

 

 

 

 

====

 

As far as I’m concerned, the three sentences in the latter paragraph are different ways of saying the same thing.

 

 

OK, let's unpack that:

 

1)

A minus prefix (e.g. '-1') is used to indicate that the group is disordered about one or more symmetry elements.

 

I am totally OK with this. I would prefer sticking to concepts involving symmetry operations, but I get it now.

 

 2)

In addition to not being occupied simultaneously with sites belonging to different groups, the atom sites of such a group are not occupied simultaneously with local symmetry equivalents of sites belonging to the same group. 

 

Maybe. I just have never heard of "local symmetry equivalents" -- that is completely new to me. But if that is what people say, OK.

 

 3)

That is, some of the group's symmetry equivalents are among its disorder complements.

 

Not sure this one is needed.

 

 

I guess I would just say that if this were the description, and it makes sense to crystallographers, and that is our audience, perhaps that is an improvement. I can't say, because I am not a crystallographer. If I had read that, I would probably have had to ask Brian the same question, because I wouldn't know what a "local symmetry element" is. ;)

 

BTW, the "software rendering" addition I was suggesting was from the SHELX manual, which Brian quoted to me:

 

And from http://xrayweb.chem.ou.edu/notes/manuals/shelxl_user_guide.pdf:

"...the generation of equivalents (e.g. in a toluene molecule on
an inversion center) may be prevented by assigning a negative PART
number."

 

I understand the reason for not getting into rendering in the CIF description. Still, someone working on Mercury apparently had the same problem understanding this "-n" designation. Thus, maybe there is some argument for at least mentioning bonding. Or not.

 

I think the addition of "local" does technically correct the issue I had with John's suggested change.

 

Bob

 



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