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Re: Ambiguity in atom_site.disorder_group value -1

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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