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cif_ed.dic
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#\#CIF_2.0
##############################################################################
# #
# CIF Electron Diffraction Dictionary #
# #
# This draft dictionary contains names and definitions of data items used #
# especially in describing structures determined by electron diffraction. #
# #
##############################################################################
data_CIF_ED
_dictionary.title CIF_ED
_dictionary.class Instance
_dictionary.version 1.0.1-dev
_dictionary.date 2025-03-24
_dictionary.uri
https://raw.githubusercontent.com/COMCIFS/cif_ed/main/cif_ed.dic
_dictionary.ddl_conformance 4.2.0
_dictionary.namespace CifCore
_description.text
;
This dictionary defines data items used to specify the aspects of
crystal structures determined by electron diffraction specific to
that technique.
;
loop_
_dictionary_author.id
_dictionary_author.id_ORCID
_dictionary_author.name
_dictionary_author.email
1 0000-0002-8987-8164 'Palatinus, LukΓ‘Ε‘' [email protected]
2 0000-0002-7367-4343 'Santucci, Marco' [email protected]
3 0000-0002-9042-8603 'Suresh, Ashwin' [email protected]
save_CIF_ED_HEAD
_definition.id CIF_ED_HEAD
_definition.scope Category
_definition.class Head
_definition.update 2024-05-15
_description.text
;
This category is the Head category for an extension dictionary used for
crystallographic structure determination using electron diffraction.
;
_name.category_id CIF_ED
_name.object_id CIF_ED_HEAD
_import.get
[
{'dupl':Ignore 'file':cif_core.dic 'mode':Full 'save':CIF_CORE_HEAD}
]
save_
save_chemical.absolute_configuration
_definition.id '_chemical.absolute_configuration'
_alias.definition_id '_chemical_absolute_configuration'
_definition.update 2024-04-22
_description.text
;
Necessary conditions for this assignment are given by
Flack, H. D. & Bernardinelli, G. (1999). Acta Cryst. A55, 908-915.
https://doi.org/10.1107/S0108767399004262
https://www.iucr.org/paper?sh0129
Flack, H. D. & Bernardinelli, G. (2000). J. Appl. Cryst. 33, 1143-1148.
https://doi.org/10.1107/S0021889800007184
https://www.iucr.org/paper?ks0021
;
_name.category_id chemical
_name.object_id absolute_configuration
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Text
loop_
_enumeration_set.state
_enumeration_set.detail
rm
;
'reference molecule' Absolute configuration established by the
structure determination of a compound containing a chiral reference
molecule of known absolute configuration.
;
ad
;
'anomalous dispersion' Absolute configuration established by a-d
effects in diffraction measurements on the crystal.
;
dyn
;
Absolute configuration determined directly from dynamical refinement.
;
rmad
;
'rm + ad' Absolute configuration established by the structure
determination of a compound containing a chiral reference molecule of
known absolute configuration and confirmed by a-d effects in
diffraction measurements on the crystal.
;
syn
;
'synthetic' Absolute configuration has not been established by
anomalous-dispersion effects in diffraction measurements on the
crystal. The enantiomer has been assigned by reference to an
unchanging chiral centre in the synthetic procedure.
;
unk
;
'unknown' No firm chemical or a-d evidence for an assignment is
available. An arbitrary choice of enantiomer has been made.
;
.
;
Inapplicable.
;
save_
save_computing.sample_tracking
_definition.id '_computing.sample_tracking'
_definition.update 2024-07-08
_description.text
;
Reference to software used to track the position of a sample with
respect to the diffraction source beam. Typically used in 3D
electron diffraction. More details of the tracking method may be
provided in _diffrn_measurement.sample_tracking_method.
;
_name.category_id computing
_name.object_id sample_tracking
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
_description_example.case 'PyFast-ADT (Santucci, 2024)'
save_
save_diffrn.precession_semi_angle
_definition.id '_diffrn.precession_semi_angle'
_definition.update 2024-04-22
_description.text
;
Angle at the sample of the tilt from the normal direction of a radiation
beam moved in a precessional scan.
;
_name.category_id diffrn
_name.object_id precession_semi_angle
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code degrees
save_
save_diffrn.precession_semi_angle_su
_definition.id '_diffrn.precession_semi_angle_su'
_definition.update 2024-04-22
_description.text
;
Standard uncertainty of _diffrn.precession_semi_angle.
;
_name.category_id diffrn
_name.object_id precession_semi_angle_su
_name.linked_item_id '_diffrn.precession_semi_angle'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_units.code degrees
save_
save_diffrn_measurement.method_precession
_definition.id '_diffrn_measurement.method_precession'
_definition.update 2024-05-15
_description.text
;
Yes or no flag indicating if the radiation beam illuminates the sample
at an angle that is rotated about a precession axis.
;
_name.category_id diffrn_measurement
_name.object_id method_precession
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
yes 'Precession method is used.'
y 'Abbreviation for "yes".'
no 'Precession method is not used.'
n 'Abbreviation for "no".'
save_
save_diffrn_measurement.rotation_mode
_definition.id '_diffrn_measurement.rotation_mode'
_definition.update 2024-12-02
_description.text
;
Code describing the technique used to sample as completely as possible
the accessible range of reciprocal space.
;
_name.category_id diffrn_measurement
_name.object_id rotation_mode
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
rotation
;
The detector records diffracted intensities continuously while the
sample is rotated.
;
stepwise
;
The detector records diffracted intensities while the sample
is stationary and the beam is either steady or performing a
defined motion, typically precessing around a conical surface
normal to the sample (precession electron diffraction).
;
save_
save_diffrn_measurement.sample_tracking
_definition.id '_diffrn_measurement.sample_tracking'
_definition.update 2024-07-25
_description.text
;
Yes or no flag indicating if a tracking method to follow the
crystal was used in the data acquisition. Typically used to track
very small crystals in electron diffraction experiments.
;
_name.category_id diffrn_measurement
_name.object_id sample_tracking
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
yes 'A crystal tracking method is used.'
y 'Abbreviation for "yes".'
no 'A crystal tracking method is not used.'
n 'Abbreviation for "no".'
save_
save_diffrn_measurement.sample_tracking_method
_definition.id '_diffrn_measurement.sample_tracking_method'
_definition.update 2024-07-25
_description.text
;
Description of the method used to follow the crystal during data collection.
;
_name.category_id diffrn_measurement
_name.object_id sample_tracking_method
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
_description_example.case 'Electron-beam tracking by PyFast-ADT'
save_
save_diffrn_radiation.illumination_mode
_definition.id '_diffrn_radiation.illumination_mode'
_definition.update 2024-05-15
_description.text
;
Code describing the optical configuration of the incident beam at
the sample. For electron diffraction, parallel illumination is
the normal mode in transmission electron microscopy (TEM),
convergent-beam in scanning transmission electron microscopy
(STEM).
;
_name.category_id diffrn_radiation
_name.object_id illumination_mode
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
convergent 'Convergent-beam illumination'
parallel 'Parallel illumination'
save_
save_diffrn_source.convergence_angle
_definition.id '_diffrn_source.convergence_angle'
_definition.update 2024-07-11
_description.text
;
The angle of convergence of the source beam (for example in
convergent-beam electron diffraction). The convergence angle
is the angular spread of the cone of illumination (i.e. 2Ξ±,
where the semi-angle Ξ± is measured from the axis defining the
beam direction).
;
_name.category_id diffrn_source
_name.object_id convergence_angle
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code degrees
save_
save_diffrn_source.ed_diffracting_area_selection
_definition.id '_diffrn_source.ed_diffracting_area_selection'
_definition.update 2024-12-02
_description.text
;
Enumerated code for the technique in electron diffraction used to
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
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Text
loop_
_enumeration_set.state
_enumeration_set.detail
probe 'Diffraction region selected by the size of the probe (= beam)'
SAED 'Selected-area electron diffraction'
save_
save_diffrn_source.size
_definition.id '_diffrn_source.size'
_alias.definition_id '_diffrn_source_size'
_definition.update 2012-11-26
_description.text
;
Description of the collimated source beam as viewed from the sample.
;
_name.category_id diffrn_source
_name.object_id size
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'8mm x 0.4 mm fine-focus'
'broad focus'
'300 nm electron beam in NBED (nano-beam electron diffraction)'
'1 micrometre aperture size in SAED (selected-aperture el. diffr.)'
save_
save_exptl_crystal.mosaic_block_size
_definition.id '_exptl_crystal.mosaic_block_size'
_definition.update 2024-07-22
_description.text
;
Isotropic and resolution-independent term representing the average size of
mosaic domains in the crystal specified in angstroms. Larger size indicates
better ordered crystals.
;
_name.category_id exptl_crystal
_name.object_id mosaic_block_size
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.:
_units.code angstroms
save_
save_exptl_crystal.mosaic_block_size_su
_definition.id '_exptl_crystal.mosaic_block_size_su'
_definition.update 2024-07-22
_description.text
;
Standard uncertainty of _exptl_crystal.mosaic_block_size.
;
_name.category_id exptl_crystal
_name.object_id mosaic_block_size_su
_name.linked_item_id '_exptl_crystal.mosaic_block_size'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_units.code angstroms
save_
save_exptl_crystal.mosaic_method
_definition.id '_exptl_crystal.mosaic_method'
_definition.update 2024-05-07
_description.text
;
How parameters derived from the spot shape (such as mosaic block
size and rotation, beam divergence, and crossfire) and their
errors were estimated.
This can be a written description or a citation to a specific
software package that determined these parameters.
;
_name.category_id exptl_crystal
_name.object_id mosaic_method
_type.purpose Describe
_type.source Derived
_type.container Single
_type.contents Text
_description_example.case 'Determined from rocking curve.'
save_
save_exptl_crystal.mosaicity
_definition.id '_exptl_crystal.mosaicity'
_definition.update 2024-07-09
_description.text
;
Isotropic approximation of the distribution of mis-orientation angles
specified in degrees of all the mosaic domain blocks in the crystal,
represented as a standard deviation. Here, a mosaic block is a set of
contiguous unit cells assumed to be perfectly aligned. Lower mosaicity
indicates better ordered crystals. See for example:
Nave, C. (1998). Acta Cryst. D54, 848-853.
Note that many software packages estimate the mosaic rotation distribution
differently and may combine several physical properties of the experiment
into a single mosaic term. This term will help fit the modelled spots
to the observed spots without necessarily being directly related to the
physics of the crystal itself.
;
_name.category_id exptl_crystal
_name.object_id mosaicity
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.:
_units.code degrees
save_
save_exptl_crystal.mosaicity_su
_definition.id '_exptl_crystal.mosaicity_su'
_definition.update 2024-07-09
_description.text
;
Standard uncertainty of _exptl_crystal.mosaicity.
;
_name.category_id exptl_crystal
_name.object_id mosaicity_su
_name.linked_item_id '_exptl_crystal.mosaicity'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_units.code degrees
save_
save_refine_diff.potential_max
_definition.id '_refine_diff.potential_max'
_definition.update 2024-12-06
_description.text
;
Maximum electrostatic potential value in a difference Fourier map.
;
_name.category_id refine_diff
_name.object_id potential_max
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_units.code electrons_per_angstrom
save_
save_refine_diff.potential_max_su
_definition.id '_refine_diff.potential_max_su'
_definition.update 2024-12-06
_description.text
;
Standard uncertainty of _refine_diff.potential_max.
;
_name.category_id refine_diff
_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
_units.code electrons_per_angstrom
save_
save_refine_diff.potential_min
_definition.id '_refine_diff.potential_min'
_definition.update 2024-12-06
_description.text
;
Minimum electrostatic potential value in a difference Fourier map.
;
_name.category_id refine_diff
_name.object_id potential_min
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_units.code electrons_per_angstrom
save_
save_refine_diff.potential_min_su
_definition.id '_refine_diff.potential_min_su'
_definition.update 2024-12-06
_description.text
;
Standard uncertainty of _refine_diff.potential_min.
;
_name.category_id refine_diff
_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
_units.code electrons_per_angstrom
save_
save_refine_diff.potential_rms
_definition.id '_refine_diff.potential_RMS'
_definition.update 2024-12-06
_description.text
;
Root mean square electrostatic potential value in a difference Fourier map.
This value is measured with respect to the arithmetic mean
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 potential_RMS
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_units.code electrons_per_angstrom
save_
save_refine_diff.potential_rms_su
_definition.id '_refine_diff.potential_RMS_su'
_definition.update 2024-12-06
_description.text
;
Standard uncertainty of _refine_diff.potential_RMS.
;
_name.category_id refine_diff
_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
_units.code electrons_per_angstrom
save_
save_refine.diffraction_theory
_definition.id '_refine.diffraction_theory'
_definition.update 2024-05-15
_description.text
;
A code describing the approach to the calculation of the
diffracted intensities. In the kinematical approximation,
interactions of diffracted waves with matter are neglected, and
integrated intensities of the Bragg reflections are proportional
to the square of the modulus of the structure factor. In the
dynamical calculation, interactions between diffracted waves are
taken into account, and the proportionality of the intensities and
the structure factors is not preserved.
;
_name.category_id refine
_name.object_id diffraction_theory
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
dynamical
;
Interactions between diffracted waves and matter are taken into
account when calculating the amplitudes of the diffracted beams.
;
kinematical
;
Interactions between diffracted waves and matter are ignored
when calculating the amplitudes of diffracted beams.
;
save_
save_refine.diffraction_theory_details
_definition.id '_refine.diffraction_theory_details'
_definition.update 2024-12-02
_description.text
;
Details needed to characterize the approach to the calculation of the
diffracted intensities, such as a description of the parameters that
were refined dynamically.
;
_name.category_id refine
_name.object_id diffraction_theory_details
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save_refine_ls.abs_structure_z-score
_definition.id '_refine_ls.abs_structure_z-score'
_definition.update 2024-05-03
_description.text
;
The z-score is a measure of confidence in an absolute structure
determination as described by Klar et al. (2023), based on the
method of Le Page et al. (1990). For centrosymmetric structures,
the only permitted value, if the data item is present, is
'inapplicable', represented by '.' .
Ref: Klar, P. B. et al. (2023). Nature Chem. 15, 848-855.
Le Page, Y., Gabe, E. J. & Gainsford, G. J. (1990). J. Appl. Cryst.
23, 406-411.
;
_name.category_id refine_ls
_name.object_id abs_structure_z_score
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_units.code none
save_
save_refine_ls.sample_shape_details
_definition.id '_refine_ls.sample_shape_details'
_definition.update 2024-07-25
_description.text
;
Additional details describing the sample thickness when calculated
during dynamical refinement where this cannot be defined completely by
the formula given in _refine_ls.sample_shape_expression.
Ref: Palatinus, L., Petricek, V. & Correa, C. A. (2015). Acta
Cryst. A71, 235-244.
;
_name.category_id refine_ls
_name.object_id sample_shape_details
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save_refine_ls.sample_shape_expression
_definition.id '_refine_ls.sample_shape_expression'
_definition.update 2024-07-25
_description.text
;
Formula for the sample thickness distribution when the sample
thickness is considered during dynamical refinement.
Ref: Palatinus, L., Petricek, V. & Correa, C. A. (2015). Acta
Cryst. A71, 235-244.
;
_name.category_id refine_ls
_name.object_id sample_shape_expression
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
_description_example.case
;
F(π) = 1 - ( 1 - π^2^)^1/2^
;
_description_example.detail
;
The cumulative distribution function in terms of the reduced thickness π
of a sample treated as a cylinder. π = t/t~m~, where t is the thickness
at the point illuminated and t~m~ the maximum thickness of the cylinder
(i.e. its diameter).
;
save_
save_refine_ls.sample_thickness
_definition.id '_refine_ls.sample_thickness'
_definition.update 2024-07-08
_description.text
;
The refined sample thickness as determined by dynamical refinement.
Ref: Palatinus, L., Petricek, V. & Correa, C. A. (2015). Acta
Cryst. A71, 235-244.
;
_name.category_id refine_ls
_name.object_id sample_thickness
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.:
_units.code nanometres
_description_example.case 35(2)
save_
save_refine_ls.sample_thickness_su
_definition.id '_refine_ls.sample_thickness_su'
_definition.update 2024-07-08
_description.text
;
Standard uncertainty of _refine_ls.sample_thickness.
;
_name.category_id refine_ls
_name.object_id sample_thickness_su
_name.linked_item_id '_refine_ls.sample_thickness'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_units.code nanometres
save_
loop_
_dictionary_audit.version
_dictionary_audit.date
_dictionary_audit.revision
0.0.1 2024-04-18
;
Basic skeleton of dictionary set up (no definitions).
;
0.1.0 2024-05-15
;
Initial draft of new or revised (from coreCIF) data definitions
following nanED round robin project. (B. McMahon)
;
1.0.0 2025-03-24
;
Initial release version of this dictionary cif_ed.dic for electron
diffraction, developed by the NanED standards committee and with
input from the IUCr Commission on Electron Crystallography.
This dictionary is not intended to be a standalone dictionary,
but rather a platform to allow focussed development of items
specific to electron diffraction, prior to incorporation in the
core CIF or other relevant COMCIFS-managed CIF dictionaries. Some
of the definitions in this dictionary may be copies of core
definitions with extended attributes.
;
1.0.1-dev 2025-03-24
;
# Please update the date above and describe the change below until
# ready for the next release
Initialised new development version.
;