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Further changes to cif_ed.dic, docs/ed.pdf and docs/recommendations.md,
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mostlt relating to changes from _refine_diff.density_* to *.potential_*
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@nautolycus
nautolycus committed Dec 6, 2024
1 parent e45072b commit 60438c9
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201 changes: 50 additions & 151 deletions cif_ed.dic
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ data_CIF_ED
_dictionary.title CIF_ED
_dictionary.class Instance
_dictionary.version 0.1.0-dev
_dictionary.date 2024-12-02
_dictionary.date 2024-12-06
_dictionary.uri
https://raw.githubusercontent.com/COMCIFS/cif_ed/main/cif_ed.dic
_dictionary.ddl_conformance 4.2.0
Expand Down Expand Up @@ -374,8 +374,8 @@ save_diffrn_source.ed_diffracting_area_selection
_description.text
;
Enumerated code for the technique in electron diffraction used to
determine whether probe or SAED was used to illuminate the appropriate
region of the sample by the incident radiation beam.
select the region of the sample from which the diffraction pattern
is obtained.
;
_name.category_id diffrn_source
_name.object_id ed_diffracting_area_selection
Expand All @@ -388,7 +388,7 @@ save_diffrn_source.ed_diffracting_area_selection
_enumeration_set.state
_enumeration_set.detail
probe 'Diffraction region selected by the size of the probe (= beam)'
SAED 'Selected-area electron diffraction.'
SAED 'Selected-area electron diffraction'

save_

Expand Down Expand Up @@ -530,224 +530,119 @@ save_exptl_crystal.mosaicity_su

save_

save_refine_diff.density_max
save_refine_diff.potential_max

_definition.id '_refine_diff.density_max'

loop_
_alias.definition_id
'_refine_diff_density_max'
'_refine.diff_density_max'

_definition.update 2024-05-01
_definition.id '_refine_diff.potential_max'
_definition.update 2024-12-06
_description.text
;
Maximum density value in a difference Fourier map.
Maximum electrostatic potential value in a difference Fourier map.
;
_name.category_id refine_diff
_name.object_id density_max
_name.object_id potential_max
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range -100.:
_method.purpose Definition
_method.expression
;
# Default units. Applicable to X-ray and gamma radiation.
_units.code = "electrons_per_angstrom_cubed"

If (_diffrn_radiation.probe == "neutron")
_units.code = "femtometres_per_angstrom_cubed"

If (_diffrn_radiation.probe == "electron")
_units.code = "electrons_per_angstrom"
;
_units.code electrons_per_angstrom

save_

save_refine_diff.density_max_su

_definition.id '_refine_diff.density_max_su'
save_refine_diff.potential_max_su

loop_
_alias.definition_id
'_refine_diff_density_max_su'
'_refine.diff_density_max_esd'

_definition.update 2024-05-01
_definition.id '_refine_diff.potential_max_su'
_definition.update 2024-12-06
_description.text
;
Standard uncertainty of _refine_diff.density_max.
Standard uncertainty of _refine_diff.potential_max.
;
_name.category_id refine_diff
_name.object_id density_max_su
_name.linked_item_id '_refine_diff.density_max'
_name.object_id potential_max_su
_name.linked_item_id '_refine_diff.potential_max'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_method.purpose Definition
_method.expression
;
# Default units. Applicable to X-ray and gamma radiation.
_units.code = "electrons_per_angstrom_cubed"

If (_diffrn_radiation.probe == "neutron")
_units.code = "femtometres_per_angstrom_cubed"

If (_diffrn_radiation.probe == "electron")
_units.code = "electrons_per_angstrom"
;
_units.code electrons_per_angstrom

save_

save_refine_diff.density_min

_definition.id '_refine_diff.density_min'

loop_
_alias.definition_id
'_refine_diff_density_min'
'_refine.diff_density_min'
save_refine_diff.potential_min

_definition.update 2024-05-01
_definition.id '_refine_diff.potential_min'
_definition.update 2024-12-06
_description.text
;
Minimum density value in a difference Fourier map.
Minimum electrostatic potential value in a difference Fourier map.
;
_name.category_id refine_diff
_name.object_id density_min
_name.object_id potential_min
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range :100.
_method.purpose Definition
_method.expression
;
# Default units. Applicable to X-ray and gamma radiation.
_units.code = "electrons_per_angstrom_cubed"

If (_diffrn_radiation.probe == "neutron")
_units.code = "femtometres_per_angstrom_cubed"

If (_diffrn_radiation.probe == "electron")
_units.code = "electrons_per_angstrom"
;
_units.code electrons_per_angstrom

save_

save_refine_diff.density_min_su

_definition.id '_refine_diff.density_min_su'
save_refine_diff.potential_min_su

loop_
_alias.definition_id
'_refine_diff_density_min_su'
'_refine.diff_density_min_esd'

_definition.update 2024-05-01
_definition.id '_refine_diff.potential_min_su'
_definition.update 2024-12-06
_description.text
;
Standard uncertainty of _refine_diff.density_min.
Standard uncertainty of _refine_diff.potential_min.
;
_name.category_id refine_diff
_name.object_id density_min_su
_name.linked_item_id '_refine_diff.density_min'
_name.object_id potential_min_su
_name.linked_item_id '_refine_diff.potential_min'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_method.purpose Definition
_method.expression
;
# Default units. Applicable to X-ray and gamma radiation.
_units.code = "electrons_per_angstrom_cubed"

If (_diffrn_radiation.probe == "neutron")
_units.code = "femtometres_per_angstrom_cubed"

If (_diffrn_radiation.probe == "electron")
_units.code = "electrons_per_angstrom"
;
_units.code electrons_per_angstrom

save_

save_refine_diff.density_rms
save_refine_diff.potential_rms

_definition.id '_refine_diff.density_RMS'

loop_
_alias.definition_id
'_refine_diff_density_RMS'
'_refine.diff_density_RMS'

_definition.update 2024-05-01
_definition.id '_refine_diff.potential_RMS'
_definition.update 2024-12-06
_description.text
;
Root mean square density value in a difference Fourier map.
Root mean square electrostatic potential value in a difference Fourier map.
This value is measured with respect to the arithmetic mean
density and is derived from summations over each grid point
potential and is derived from summations over each grid point
in the asymmetric unit of the cell. This quantity is useful
for assessing the significance of *_min and *_max values,
and also for defining suitable contour levels.
;
_name.category_id refine_diff
_name.object_id density_RMS
_name.object_id potential_RMS
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range -100.:100.
_method.purpose Definition
_method.expression
;
# Default units. Applicable to X-ray and gamma radiation.
_units.code = "electrons_per_angstrom_cubed"

If (_diffrn_radiation.probe == "neutron")
_units.code = "femtometres_per_angstrom_cubed"

If (_diffrn_radiation.probe == "electron")
_units.code = "electrons_per_angstrom"
;
_units.code electrons_per_angstrom

save_

save_refine_diff.density_rms_su

_definition.id '_refine_diff.density_RMS_su'

loop_
_alias.definition_id
'_refine_diff_density_RMS_su'
'_refine.diff_density_RMS_esd'
save_refine_diff.potential_rms_su

_definition.update 2024-05-01
_definition.id '_refine_diff.potential_RMS_su'
_definition.update 2024-12-06
_description.text
;
Standard uncertainty of _refine_diff.density_RMS.
Standard uncertainty of _refine_diff.potential_RMS.
;
_name.category_id refine_diff
_name.object_id density_RMS_su
_name.linked_item_id '_refine_diff.density_RMS'
_name.object_id potential_RMS_su
_name.linked_item_id '_refine_diff.potential_RMS'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_method.purpose Definition
_method.expression
;
# Default units. Applicable to X-ray and gamma radiation.
_units.code = "electrons_per_angstrom_cubed"

If (_diffrn_radiation.probe == "neutron")
_units.code = "femtometres_per_angstrom_cubed"

If (_diffrn_radiation.probe == "electron")
_units.code = "electrons_per_angstrom"
;
_units.code electrons_per_angstrom

save_

Expand Down Expand Up @@ -961,7 +856,7 @@ save_
Updated the CIF_CORE dictionary import statement with the new Head
category name.
;
0.1.0-dev 2024-12-02
0.1.0-dev 2024-12-06
;
Changed the version number to 0.1.0-dev to indicate this is a
development version. Still under discussion as to whether this will
Expand Down Expand Up @@ -997,5 +892,9 @@ save_
definition and enumeration list; added
_refine.diffraction_theory_details; renamed
_diffrn_measurement.integration as _diffrn_measurement.rotation_mode
and revised enumeration list;
and revised enumeration list.

Introduced _refine_diff.potential_max, *_min, *_RMS and associated
SU values (replacing updated REFINE_DIFF density terms) to reflect
correct practice in ED. (bm/Lukas)
;
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4 changes: 2 additions & 2 deletions docs/recommendations.md
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Original file line number Diff line number Diff line change
Expand Up @@ -80,9 +80,9 @@ The number of crystals used in the measurement of intensities should be specifie

The enumerated data item `_refine.diffraction_theory` can take the values 'dynamical' and 'kinematical', and should always be specified if refinement is performed using the dynamical theory. `_refine.diffraction_theory_details` is a free-text field where _e.g._ a description may be given of the parameters that were refined dynamically.

### `refine_diff.density_max`, `_min` and `_RMS`
### `_refine_diff.potential_max`, `_min` and `_RMS`

These quantities were defined in the original core CIF dictionary as indications of the final difference electron density. For electron diffraction, they should report the maximum, minimum and mean difference potential in the final difference Fourier map, and be expressed in units of electrons per ångström.
These quantities are similar to those defined in the original core CIF dictionary describing features of the final difference electron density (_refine_diff.density_max` _etc._). For electron diffraction, they report the maximum, minimum and mean residual electrostatic potential in the final difference Fourier map, and are expressed in units of electrons per ångström.

### `_refine_ls.abs_structure_z-score`

Expand Down

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