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RE: Ambiguity in atom_site.disorder_group value -1

Hi Bob,

 

My query is really not about documentation language. What I'm interested in is the way the -1 value should be interpreted.

 

Ok.

 

it is easy to translate that into the PDB (and Jmol's) "altloc" concept. We have two "configurations" -- "configuration=1" is all non-disordered atoms along with the first disorder_group (1 here); "configuration=2" is all the non-disordered atoms along with the second disorder_group (2 here).

 

But this seems not possible when -1 is used, and we just let the space group's N symmetry operations create all the replicas. I just have a list of N distinct groups.

 

In this kind of disorder, the disordered group’s alternative location does not have its own independent coordinates.  The coordinates of the two (or more) locations are related by a symmetry operation (because the groups are near one or more symmetry elements of the space group).  I can well imagine that that would play poorly with PDB’s or JMol’s altloc mechanism, though I have not personally written code that touches that particular area.

 

The usual approach for computing connectivity in such cases is to ignore all symmetry operations when computing connections within such a disordered group.

 

What I would be interested in is some way in the CIF to be able to describe this "localness" of the disorder. That, for example, the results of symop 1 and symop 2 are paired. And, likewise, in this case I presented, symops paired as [1,2], [3,4], [5,6], and [7,8]. Wouldn't this be useful information?

 

I can imagine that there might be uses for such information, but I can’t think of any for typical visualization scenarios.  Perhaps it would be interesting for automating details of report generation, or such.  There are some caveats, however, among them,

 

  • The specific symmetry operation relating the coordinates expressed in the CIF to those of their particular local disorder complement(s) is not necessarily one of those enumerated in the CIF.  It might instead be a composition of one those with a lattice translation or a centering translation.
  • The groupings are derivable from other information in the CIF.  That doesn’t necessarily mean that they should not be presented (certainly other derived data are presented), but it does mean that no information is lost by omitting them.
  • I’m not aware of anything that presently computes or outputs such groupings, so I’m skeptical about the prospects for data items describing them actually being populated.

 

 

 

[…] Would that be a reasonable feature request?

 

I presume that the proposal would not have been presented if you didn’t have plans for how JMol would use such items.  If we can establish that there are sources that compute these data or would be willing to do so, and that would output them into CIF if there were data items with which to express them, then I would be open to talking about particulars.

 

 

Best regards,

 

John

 

From: Robert Hanson <hansonr@stolaf.edu>
Sent: Wednesday, October 19, 2022 6:01 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.

 

Maybe more to the point, here. My query is really not about documentation language. What I'm interested in is the way the -1 value should be interpreted. Disorder has always been a bit messy, but there are mechanism in the standard way of describing disorder to identify the "local" sets (pairs, usually) of incompatible (overlapping) disorder options. The groups might be listed as 1 and 2, for example:

 

loop_
 _atom_site_label
 _atom_site_type_symbol
 _atom_site_fract_x
 _atom_site_fract_y
 _atom_site_fract_z
 _atom_site_U_iso_or_equiv
 _atom_site_adp_type
 _atom_site_occupancy
 _atom_site_symmetry_multiplicity
 _atom_site_calc_flag
 _atom_site_refinement_flags
 _atom_site_disorder_assembly
 _atom_site_disorder_group
C5 C 0.0734(6) 0.1405(6) 0.4244(5) 0.046(4) Uani 0.50 1 d PD A 1
F7 F 0.0566(11) 0.0602(8) 0.4658(8) 0.059(3) Uiso 0.50 1 d PD A 1
F8 F 0.1048(9) 0.1116(10) 0.3518(6) 0.050(3) Uiso 0.50 1 d PD A 1
F9 F -0.0186(7) 0.1756(10) 0.4124(8) 0.044(3) Uiso 0.50 1 d PD A 1
C5' C 0.0734(6) 0.1405(6) 0.4244(5) 0.046(4) Uani 0.50 1 d PD A 2
F7' F 0.1110(9) 0.0547(7) 0.4085(9) 0.044(3) Uiso 0.50 1 d PD A 2
F8' F 0.0692(10) 0.1827(10) 0.3517(7) 0.059(3) Uiso 0.50 1 d PD A 2
F9' F -0.0222(6) 0.1262(10) 0.4446(8) 0.050(3) Uiso 0.50 1 d PD A 2

 

where it is easy to translate that into the PDB (and Jmol's) "altloc" concept. We have two "configurations" -- "configuration=1" is all non-disordered atoms along with the first disorder_group (1 here); "configuration=2" is all the non-disordered atoms along with the second disorder_group (2 here).

 

But this seems not possible when -1 is used, and we just let the space group's N symmetry operations create all the replicas. I just have a list of N distinct groups.

 

What I would be interested in is some way in the CIF to be able to describe this "localness" of the disorder. That, for example, the results of symop 1 and symop 2 are paired. And, likewise, in this case I presented, symops paired as [1,2], [3,4], [5,6], and [7,8]. Wouldn't this be useful information?

 

I think it would be an extension of the

 

 _atom_site_disorder_assembly
 _atom_site_disorder_group 

 

idea, but listing symmetry operations. Perhaps something like:

 

loop_

_local_disorder_id

_local_disorder_assembly  # matches atom_site_disorder_assembly

_local_disorder_group  # matches atom_site_disorder_group

_local_disorder_assembly_symmetry_operation_set   #matches list of space_group_symop_id

1 A -1 1,2

2 A -1 3,4

3 A -1 5,6

4 A -1 7,8

 

corresponding to the disorder-1.cif that I provided in a previous message. With documentation something like:

 

Category local_disorder

 

Category description

 

The local_disorder category identifies sets of symmetry operations that, when applied to sites in the asymmetric unit identified using a negative number for atom_site_disorder_group, generate local (that is, independent) sets of disordered groups.

Would that be a reasonable feature request?

 

Bob



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