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CIF-core: Proposed revisions

  • To: Multiple recipients of list <coredmg@iucr.org>
  • Subject: CIF-core: Proposed revisions
  • From: "I. David Brown" <idbrown@mcmail.cis.mcmaster.ca>
  • Date: Tue, 23 Jul 2002 15:09:59 +0100 (BST)
Dear Colleagues,

	In order to focus our attention on the current round of revisions
to the CIF core dictionary, I have attached a copy of some proposed
dictionary code.  This is an extensive list, but most of it should
be uncontroversial and therefore we should be able to approve most of the
items with little discussion.  The more difficult items I will introduce
later, once we have the more straightforward items out of the way.

	One set of items has already been approved but not yet
incorporated into the dictionary, hence they are included in the attached
document with the status of 'approved'.  The others are now open for
discussion.  Since we are in the middle of holiday time (in the northern
hemisphere) and the Geneva Congress is approaching, I don't expect much
activity on this discussion group until the end of August.  If the group
does not then swing into activity, I will call for discussion and approval
of each item one at a time.  This will focus the discussion so that we can
work our way steadily through the agenda.

	Perhaps Brian McMahon can put this document on the web and keep it
up to date as each item is approved (or modified).  We can then all
consult the appropriate part of the document as I call for votes on each
item in turn.

	Enjoy the rest of the summer - I hope to see many of you in
Geneva.

			David


*****************************************************
Dr.I.David Brown,  Professor Emeritus
Brockhouse Institute for Materials Research,
McMaster University, Hamilton, Ontario, Canada
Tel: 1-(905)-525-9140 ext 24710
Fax: 1-(905)-521-2773
idbrown@mcmaster.ca
*****************************************************

##################################################

# 

#    PROPOSED NEW DEFINITIONS FOR CIF_CORE_2.3.DIC

#

##################################################

#

# The following items are being proposed for inclusion in 

# version 2.3 of the Core CIF dictionary.  Each item is

# followed by a comment, explaining the rational for the 

# proposal, and an indication of its status.  As each item

# is approved, approval and the date of approval will be shown

# under the status.  Any approved item will be included in the

# new version of the dictionary. 

#

# This file contains the items that are relatively uncomplicated and

# that we should be able to approve without much trouble.  Once these 

# are out of the way we can then turn our attention to the more complex

# problems in the suggested agenda, viz:

#  1. Phase transition temperatures

#  2.1 to 2.4. Items dealing with disorder, rigid groups and those in the

#      _atom_type category

#  5.2 Descriptions of peptide sequences.  As CCDC will use internal names,

#       this item is now deleted.

#  5.3 Description of crystal properties (may not be needed).

#  9.1 Twinning (awaiting the recommendations of a subcommittee)

#  9.4 definition of the diffraction orientation matrix

#  9.5 Flag for systematic absences

#  9.6 should the target be included in _diffrn_radiation rather than

#       _*_source?

#  9.7 Standards for area detectors?

#  10.1 sample history and crystal growth

#  11.1 bond multiplicity

#  14.1 details of calculation of Fcalc

#  14.2 R factor for restrained refinement

#  14.3 Twinning (see 9.1)

#  17   Adoption of Space group category

#

# The following new datanames are proposed in this draft of the revisions to

# the core dictionary.

#

#     ATOM SITE

#        _atom_site_fract_ (modify)

#        _atom_site_refinement_flags (replace with the following)

#        _atom_site_refinement_flags_posn

#        _atom_site_refinement_flags_adp

#        _atom_site_refinement_flags_occupancy

#    ATOM SITES

#       _atom_sites_special_details

#     CELL

#        _cell_reciprocal_angle_alpha

#        _cell_reciprocal_angle_beta

#        _cell_reciprocal_angle_gamma

#        _cell_formula_units_Z

#        _cell_reciprocal_length_a

#        _cell_reciprocal_length_b

#        _cell_reciprocal_length_c

#     CHEMICAL

#        _chemical_melting_point_gt

#        _chemical_melting_point_lt

#        _chemical_properties_biological

#        _chemical_properties_physical

#        _chemical_temperature_decomposition

#        _chemical_temperature_decomposition_gt

#        _chemical_temperature_decomposition_lt

#        _chemical_temperature_sublimation

#        _chemical_temperature_sublimation_gt

#        _chemical_temperature_sublimation_lt

#     CITATION

#        _citation_database_id_CSD

#     DATABASE

#        _database_code_depnum_ccdc_fiz

#        _database_code_depnum_ccdc_journal

#        _database_code_depnum_ccdc_archive

#        _database_CSD_history

#     DIFFRN

#        _diffrn_ambient_pressure_gt

#        _diffrn_ambient_pressure_lt

#        _diffrn_ambient_temperature_gt

#        _diffrn_ambient_temperature_lt

#     DIFFRN_STANDARDS

#        _diffrn_standards_decay_%_lt

#     DIFFRN_REFLNS

#        _diffrn_reflns_measured_faction_resolution_full

#        _diffrn_reflns_measured_faction_resolution_max

#        _diffrn_reflns_resolution_full

#        _diffrn_reflns_resolution_max

#     EXPTL_CRYSTAL

#        _exptl_crystal_colour   (modification)

#        _exptl_crystal_density_meas_gt

#        _exptl_crystal_density_meas_lt

#        _exptl_crystal_density_meas_temp_gt

#        _exptl_crystal_density_meas_temp_lt

#        _exptl_crystal_recrystallization

#     PUBL

#        _publ_contact_author_id_iucr

#     PULB_AUTHOR

#        _publ_author_id_iucr

#     REFINE

#        _refine_ls_extinction_coef

#        _refine_ls_extinction_coef_Zach

#        _refine_ls_extinction_coef_Becker-Coppens_1

#        _refine_ls_extinction_coef_Becker-Coppens_2

#        _refine_ls_extinction_BC_type

#        _refine_ls_extinction_expression

#        _refine_ls_extinction_method

#        _refine_ls_shift/su_max_lt

#        _refine_ls_shift/su_mean_lt

#

##################################################



##################################################

#

#   ATOM SITE

#

##################################################



data_atom_site_fract_

    loop_ _name                '_atom_site_fract_x'

                               '_atom_site_fract_y'

                               '_atom_site_fract_z'

    _category                    atom_site

    _type                        numb

    _type_conditions             esd

    _related_item              '_atom_site_Cartn_'

    _related_function            alternate

    _list                        yes

    _list_reference            '_atom_site_label'

#    _enumeration_default         0.0

    _definition

;              Atom site coordinates as fractions of the _cell_length_ values.

;

# COMMENT: The default should be deleted since it makes no sense.  If the

# coordinates are defaulted it is, presumably, because they are not known, not

# because the atom is at the origin.

# STATUS: Open for discussion



#data_atom_site_refinement_flags

#    _name                      '_atom_site_refinement_flags'

#    _category                    atom_site

#    _type                        char

#    _list                        yes

#    _list_reference            '_atom_site_label'

#    loop_ _enumeration

#          _enumeration_detail   . 'no refinement constraints'

#                                S 'special position constraint on site'

#                                G 'rigid group refinement of site'

#                            R 'riding-atom site attached to non-riding atom'

#                                D 'distance or angle restraint on site'

#                                T 'thermal displacement constraints'

#                                U 'Uiso or Uij restraint (rigid bond)'

#                                P 'partial occupancy constraint'

#    _definition

#;            A concatenated series of single-letter codes which indicate the

#               refinement restraints or constraints applied to this site.

#;



# COMMENT: The proposal is to replace this item by the following three.  The

# problem with the current definition is that it requires the character field

# to be parsed since any of the seven flags may appear in any order.  The

# replacement items define unique flags for each possibility.

# STATUS: Open for discussion



data_atom_site_refinement_flags_posn

    _name                      '_atom_site_refinement_flags_posn'

    _category                    atom_site

    _type                        char

    _list                        yes

    _list_reference            '_atom_site_label'

    loop_ _enumeration

          _enumeration_detail . 'no refinement constraints'

                              D 'distance or angle restraint on site'

                              G 'rigid group refinement of site'

                              R 'riding-atom site attached to non-riding atom'

                              S 'special position constraint on site'

                         DG   'combination of the above constraints'

                         DR   'combination of the above constraints'

                         DS   'combination of the above constraints'

                         GR   'combination of the above constraints'

                         GS   'combination of the above constraints'

                         RS    'combination of the above constraints'

                         DGR  'combination of the above constraints'

                         DGS  'combination of the above constraints'

                         DRS  'combination of the above constraints'

                         GRS  'combination of the above constraints'

                         DGRS 'combination of the above constraints'

    _definition

;              A code which indicates the refinement restraints or constraints

               applied to the positional coordinates of this site.

;

# COMMENT: Are some of these flags mutually exclusive, allowing the list to be

# shortened?



data_atom_site_refinement_flags_apd

    _name                      '_atom_site_refinement_flags_adp'

    _category                    atom_site

    _type                        char

    _list                        yes

    _list_reference            '_atom_site_label'

    loop_ _enumeration

          _enumeration_detail   .  'no refinement constraints'

                                T  'atomic displacement constraints'

                                U  'Uiso or Uij restraint (rigid bond)'

                                TU 'Both constraints applied'

    _definition

;              A code which indicates the refinement restraints or constraints

               applied to this atomic displacement parameters of this site.

;

# COMMENT: Are these enumeration details clear?  What is the difference

# between these two flags?  Can both apply at the same time?



data_atom_site_refinement_flags_occupancy

    _name                      '_atom_site_refinement_flags_occupancy'

    _category                    atom_site

    _type                        char

    _list                        yes

    _list_reference            '_atom_site_label'

    loop_ _enumeration

          _enumeration_detail   . 'no refinement constraints'

                                P 'partial occupancy constraint'

    _definition

;              A code which indicates that refinement restraints or

               constraints were applied to the occupancy of this site.

;



##################################################

#

#   ATOM SITES

#

##################################################



data_atom_sites_special_details

    _name               '_atom_sites_special_details'

    _category            atom_sites         

    _type                char

    _definition

;              Additional information about the atomic coordinates not coded

               elsewhere in the CIF.

;

# COMMENT: This could be useful in transcribing comments in databases.

# STATUS:  Open for discussion



##################################################

#

#   CELL category

#

##################################################



data_cell_reciprocal_angle_

    loop_ _name                '_cell_reciprocal_angle_alpha'

                               '_cell_reciprocal_angle_beta'

                               '_cell_reciprocal_angle_gamma'

    _category                   cell

    _type                       numb

    _type_conditions            esd

    _enumeration_range          0.0:180.0

    _enumeration_default        90.0

    _units                      deg

    _units_detail              'degrees'

    _definition

;              

***** A definition is needed. A good definition is given in Burger, X-ray

 Crystallography, but my copy is currently inaccessible. *****

;

# COMMENT: Requested by CCDC

# STATUS: Open for discussion





data_cell_formula_units_Z_prime

    _name                      '_cell_formula_units_Z'

    _category                    cell

    _type                        numb

    _enumeration_range           1:

    _definition

;              The number of the formula units as specified

               by _chemical_formula_structural, _chemical_formula_moiety or

               _chemical_formula_sum in the asymmetric unit defined the the

               unit cell given in the CELL category and the 

               space group defined in the SYMMETRY or SPACE GROUP category.

;

# COMMENT: Requested by CCDC

# STATUS: Open for discussion





data_cell_reciprocal_length_

    loop_ _name                '_cell_recirpocal_length_a'

                               '_cell_reciprocal_length_b'

                               '_cell_reciprocal_length_c'

    _category                   cell

    _type                       numb

    _type_conditions            esd

    _enumeration_range          0.0:

    _units                      A^-1^

### Is this the correct convention for defining the units?

    _units_detail              'reciprocal angstroms'

    _definition

;             

*** A definition is needed (see angles above) ********

;

# COMMENT: Requested by CCDC

# STATUS: Open for discussion



###################################################

#

#   CHEMICAL category

#

###################################################



data_chemical_melting_point_lt

    _name                      '_chemical_melting_point_lt'

    _category                   chemical

    _type                       numb

    _enumeration_range          0.0:

    _units                      K

    _units_detail              'Kelvins'

    _definition

;              A temperature in Kelvins which represents an upper limit to

               the melting point, the temperature at which a crystalline solid

               changes to a liquid.  

;

# COMMENT: Introduced to allow for a maximum limit or range of temperatures to

# be given. 

# Note that _chemical_melting_point should have the _type_conditions of 'esd'

# added

# STATUS: Open for discussion



data_chemical_melting_point_gt

    _name                      '_chemical_melting_point_gt'

    _category                   chemical        

    _type                       numb

    _enumeration_range          0.0:

    _units                      K

    _units_detail              'Kelvins'

    _definition

;              A temperature in Kelvin which represents a lower limit to the

               melting point, the temperature at which a crystalline

               solid changes to a liquid.  



;

# COMMENT:  See previous item

# STATUS: Open for discussion



data__chemcial_properties_biological

    _name                      '_chemcial_properties_biological'

    _category                   chemical

    _type                       char

    _example                    ?

    _definition

;              A description of the biological properties of the material.

;

# COMMENT: Suggested by CCDC for comments found in the CSD

# STATUS: Open for discussion



data_chemcial_properties_physical

    _name                      '_chemcial_properties_physical'

    _category                   chemical

    _type                       char

    _example                    ?

    _definition

;              A description of the physical properties of the material.

;

# COMMENT: Suggested by CCDC for comments found in the CSD

# STATUS: Open for discussion



data_chemical_temperature_decomposition

    _name                      '_chemical_temperature_decomposition'

   _category                    chemical

    _type                       numb

    _type_conditions            esd

    _units                      K

    _units_detail               Kelvin

    _example                    350

    _definition

;              The temperature in Kelvin at which a solid decomposes. 

;

# COMMENT: Suggested by CCDC.

# STATUS: Open for discussion



data_chemical_temperature_decomposition_*

    loop_ _name     '_chemical_temperature_decomposition_gt'

                    '_chemical_temperature_decomposition_lt'

    _category                   chemical

    _type                       numb

    _units                      K

    _units_detail               Kelvin

    _example                    350

    _definition

;             *_lt is a temperature below which the solid is known 

              to decompose, *_gt is the a temperature above which

              the solid is known to decompose.

;

# COMMENT: Suggested by CCDC.  These two items allow a range of

# temperatures to be specified.

# STATUS: Open for discussion





data_chemical_temperature_sublimation

    _name                      '_chemical_temperature_sublimation'

   _category                    chemical

    _type                       numb

    _type_conditions            esd

    _units                      K

    _units_detail               Kelvin

    _example                    350

    _definition

;              The temperature in Kelvin at which a solid sublimes. 

;

# COMMENT: Suggested by CCDC.

# STATUS: Open for discussion



data_chemical_temperature_sublimation_*

    loop_ _name               '_chemical_temperature_sublimation_gt'

                              '_chemical_temperature_sublimation_lt'

    _category                   chemical

    _type                       numb

    _units                      K

    _units_detail               Kelvin

    _example                    350

    _definition

;             *_lt is a temperature below which the solid is known to 

              sublime, *_gt is the a temperature above which the solid

              is known to sublime.

;

# COMMENT: Suggested by CCDC.  These two items allow a range of temperatures

# to be specified.

# STATUS: Open for discussion



###################################################

#

#   CITATION category

#

###################################################



# The following item has already been approved but still needs to be

# incorporated into the dictionary.



data_citation_database_id_CSD

    _name                     '_citation_database_id_CSD'

    _category                  citation        

    _type                      char

    _list                      yes

    _list_reference           '_citation_id'

    _example                   LEKKUH

    _definition

;           Identifier ('refcode') of the database record in the Cambridge

            Structural Database containing details of the cited structure.

;

# COMMENT: Submitted by Brian McMahon

# STATUS: Approved 2001-12-03



####################################################

#

#   DATABASE Category

#

####################################################





data_database_code_depnum_ccdc_fiz

    _name                     '_database_code_depnum_ccdc_fiz'

    _category                  database

    _type                      char

    _definition

;              Deposition numbers assigned by the Fachinformatsions Zentrum

               Karlsruhe (FIZ) to files containing structural information

               archived by the Cambridge Crystallographic Centre (CCDC)

;

# COMMENT: For use in the archives of CCDC.  Submitted by CCDC

# STATUS: approved 2002-02-28



data_database_code_depnum_ccdc_journal

    _name                     '_database_code_depnum_ccdc_journal'

    _category                  database

    _type                      char

    _definition

;              Deposition numbers assigned by various journal to files

               containing structural information archived by the Cambridge

               Crystallographic Data Centre (CCDC)

;

# COMMENT: For use in the archives of CCDC.  Submitted by CCDC

# STATUS: approved 2002-02-28



data_database_code_depnum_ccdc_archive

    _name                     '_database_code_depnum_ccdc_archive'

    _category                  database

    _type                      char

    _definition

;              Deposition numbers assigned by  the Cambridge Crystallographic

               Data Centre (CCDC) to files containing structural information

               archived by the CCDC.

;



# COMMENT: For use in the archives of CCDC.  Submitted by CCDC

# STATUS: approved 2002-02-28





data _database_CSD_history

    _name                     '_database_CSD_history'

    _category                  database        

    _type                      char

    _list                      yes

    _list_reference            ?

    _example                   ?

    _definition

;              A history of changes made by Cambridge Crystallographic Data

               Centre and incorporated into the Cambridge Structural Database

               (CSD).

;

# COMMENT: Requested by the CCDC

# STATUS: Open for discussion





###########################################

#

#   DIFFRN category

#

###########################################



data_diffrn_ambient_pressure_*

    loop_    _name                      

                              '_diffrn_ambient_pressure_gt'

                              '_diffrn_ambient_pressure_lt'

    _category                  diffrn

    _type                      numb

    _type_conditions           esd

    _enumeration_range         0.0:

    _units                     kPa

    _units_detail             'kilopascals'

    _definition

;              The mean pressure in kilopascals above which (_*_gt) or below 

               which (_*_lt) the intensities were measured.

;

# COMMENT; Provides for a pressure range to be indicated.

# STATUS: Open for discussion



data_diffrn_ambient_temperature_*

    loop_       _name                      

                              '_diffrn_ambient_temperature_gt'

                              '_diffrn_ambient_temperature_lt'

    _category                  diffrn

    _type                      numb

    _type_conditions           esd

    _enumeration_range         0.0:

    _units                     K

    _units_detail             'kelvins'

    _definition

;             The mean temperature in kelvins above which (_*_gt) or below

              which (_*_lt) the intensities were measured.

;

# COMMENT: Provides for a range of temperatures to be specified.

# STATUS: Open for discussion



################################################

#

#   DIFFRN_SOURCE

#

################################################



data_diffrn_source_take-off_angle

    _name                     '_diffrn_source_take-off_angle'

    _category                  diffrn_source

    _type                      numb

    _enumeration_range         0:90

    _units                     degrees

    _example                   ?

    _definition

;              The angle between the surface of the target and the x-ray beam

               for beams generated by traditional x-ray tubes.

;

# COMMENT: Suggested by the powder DMG.

# STATUS: Open for discussion



######################################

#

#   DIFFRN_STANDARDS category

#

######################################



data_diffrn_standards_decay_%

    _name                      '_diffrn_standards_decay_%_lt'

    _category                   diffrn_standards

    _type                       numb

    _enumeration_range          :100

    _definition

;              An upper limit on the percentage decrease in the mean

               intensity of the set of standard reflections measured at the

               start of the measurement of the diffraction pattern and at the

               end. This value is used when the decay is too small to be

               detected.

;

# COMMENT: Many experiments show no detectable decay and there is no provision

# of this at the moment other than to enter 0.0.

# STATUS: Open for discussion



#################################################

#

#  DIFFRN_REFLNS

#

#################################################



data_diffrn_reflns_measured_faction_resolution_full

    _name                '_diffrn_reflns_measured_faction_resolution_full'

    _category                   diffrn_reflns         

     _list                      yes

     _type                      numb

     _enumeration_range         0:1.0

     _related_item             '_diffrn_measured_fraction_theta_full'    

     _related_function          replace   

     _definition

;         Fraction of unique (symmetry-independent) reflections measured

          out to the resolution given in _diffrn_reflns_resolution_full.

          This number should be very close to 1.0, since it represents the

          fraction of reflections measured in the part of the diffraction

          pattern that is essentially complete.

;

# COMMENT: Replacement for _diffrn_measured_fraction_theta_full, moved to a

# more appropriate category and defined in terms of resolution rather than

# angle which depends on the radiation used.

# STATUS: Open for discussion



data__diffrn_reflns_measured_faction_resolution_max

    _name                '_diffrn_reflns_measured_faction_resolution_max'

    _category                   diffrn_reflns   

     _list                      yes

     _type                      numb

     _enumeration_range         0:1.0

    _related_item              '_diffrn_measured_fraction_theta_max'

    _related_function           replace

     _definition

;         Fraction of unique (symmetry-independent) reflections measured

          out to the resolution given in _diffrn_reflns_resolution_max.

;

# COMMENT: Replacement for _diffrn_measured_fraction_theta_max, moved to a

# more appropriate category and defined in terms of resolution rather than

# angle which depends on the radiation used.

# STATUS: Open for discussion



data_diffrn_reflns_resolution_full

    _name                      '_diffrn_reflns_resolution_full'

    _category                   diffrn_reflns

    _type                       numb

    _enumeration_range          0.0:

    _units                      A^-1^

    _units_detail              'reciprocal angstroms'

    _related_item              '_diffrn_reflns_theta_full'

    _related_function           replace

    _definition

;              The resolution in reciprocal angstroms at which the measured 

               reflection count is close to complete. The fraction of unique

               reflections measured out to this resolution is given by         

               _diffrn_reflns_measured_faction_resolution_full

;

# COMMENT: Replacement for _diffrn_reflns_theta_full expressed in terms of 

# resolution rather than an angle that depends on the radiation used.

# STATUS: Open for discussion



data_diffrn_reflns_resolution_max

    _name                      '_diffrn_reflns_resolution_max'

    _category                   diffrn_reflns

    _type                       numb

    _enumeration_range          0.0:

    _units                      A^-1^

    _units_detail              'reciprocal angstroms'

    _related_item              '_diffrn_reflns_theta_max'

    _related_function           replace

    _definition

;              Maximum resolution of the measured diffraction pattern.

;

# COMMENT: Replacement for _diffrn_reflns_theta_max expressed in terms of 

# resolution rather than an angle that depends on the radiation used.

# STATUS: Open for discussion





#################################################

#

#  EXPTL_CRYSTAL

#

#################################################



data_exptl_crystal_colour

    _name                      '_exptl_crystal_colour'

    _category                   exptl_crystal

    _type                       char

    _list                       both

    _list_reference            '_exptl_crystal_id'

loop_    _example                    

                  dark_green

                  reddish_orange_metallic

    _definition

;             The colour of the crystal used in the experiment.  The 

               following list of standardized names developed for the

               International Center for Diffraction Data should be used. 

               Combinations of descriptors should be linked by an underscore.



              The allowed colours are: colourless, white, black, gray, brown,

               red, pink, orange, yellow, green, blue, violet.  

              Colours may be modified by using one of the prefixes: light,

               dark, whitish, blackish, grayish, brownish,reddish, pinkish,

               orangish, yellowish, greenish, bluish.

              Intermediate hues may be indicated by linking two colours,

               e.g. blue_green or bluish_green

              Metallic colours are indicated by adding 'metallic' as a suffix,

               e.g. reddish_orange_metallic for copper.

;

# COMMENT: This scheme is based on a scheme developed by the ICDD and

# recommended for use in the powder CIF.  It is already checked

# in submissions to Acta Cryst.  It would be helpful to have it as part of the

# dictionary description, though it is difficult to define an enumeration list

# for the colours.

# STATUS: Open for discussion



data_exptl_crystal_density_meas_*

    loop_    _name  

                               '_exptl_crystal_density_meas_gt'

                               '_exptl_crystal_density_meas_lt'

    _category                   exptl_crystal

    _type                       numb

    _type_conditions            esd

    _list                       both

    _list_reference            '_exptl_crystal_id'

    _enumeration_range          0.0:

    _units                      Mg^-3^

    _units_detail              'megagrams per cubic metre'

    _definition

;              The lower (_*_gt) or upper limit (_*_lt) on the value of the

               density measured using standard chemical and physical

               methods. The units are megagrams per cubic metre (grams per

               cubic centimetre).

;



data_exptl_crystal_density_meas_temp_*

    loop_

         _name                 '_exptl_crystal_density_meas_temp_gt'

                               '_exptl_crystal_density_meas_temp_lt'

    _category                   exptl_crystal

    _type                       numb

    _type_conditions            esd

    _list                       both

    _list_reference            '_exptl_crystal_id'

    _enumeration_range          0.0:

    _units                      K

    _units_detail              'Kelvins'

    _definition

;              Temperature in kelvins above which (_*_gt) or below which

               (_*_lt)_exptl_crystal_density_meas was determined.

;

# COMMENT: Suggested by CCDC.

# STATUS: Open for discussion



data_exptl_crystal_recrystallization

    _name                      '_exptl_crystal_recrystallization'

    _category                   exptl_crystal        

    _type                       char

    _example                    ?

    _definition

;              Describes the method used to recrystallize the sample

;

# COMMENT: Suggested by CCDC.

# STATUS: Open for discussion





##########################################################

#

#    PUBL category

#

##########################################################



data_publ_contact_author_id_iucr

    _name                      '_publ_contact_author_id_iucr'

    _category                   publ        

    _type                       char    

    _list                       yes    

    _example                    2985

    _definition

;              Identifier in the IUCr contact database of the author

               submitting the manuscript and datablock.  This identifier may

               be available from the World Directory of Crystallographers

               (http://wdc.iucr.org).

;



# COMMENT: Submitted by Brian McMahon  This identifier will allow linking to

# other publications or files by the contact author. 

# (Linking based on name alone is inefficient because

# individuals change their names or spelling of the names.  A complementary

# data name is proposed for the authors in the PUBL_AUTHOR category.

# STATUS: Open for discussion



#########################################################

#

#   PUBL_AUTHOR category

#

#########################################################



data_publ_author_id_iucr

    _name                      '_publ_author_id_iucr'

    _category                   publ_author

    _type                       char

    _list                       yes

    _example                    2985

    _definition

;              Identifier in the IUCr contact database of a publication

               author.  This identifier may be available from the World

               Directory of Crystallographers (http://wdc.iucr.org).

;



# COMMENT: Submitted by Brian McMahon.  See _publ_contact_author_id_iucr for

# further details.

# STATUS: Open for discussion





#########################################

#

#   REFINE category

#

#########################################



# The next five items relate to extinction and are an attempt to tighten up

# our definitions.



data_refine_ls_extinction_coef

    _name                      '_refine_ls_extinction_coef'

    _category                    refine

    _type                        numb

    _type_conditions             esd

    _example                     3472(52)

    _example_detail             'Zachariasen coefficient r* = 0.347(5) E04'

    _definition

;              The extinction coefficient used to calculate the correction

               factor applied to the structure-factor data. The nature of the

               extinction coefficient is given in the definitions of

               _refine_ls_extinction_expression and

               _refine_ls_extinction_method.



               For the 'Zachariasen' method it is the r* value; for the

               'Becker-Coppens type 1 isotropic' method it is the 'g' value,

               and for 'Becker-Coppens type 2 isotropic' corrections it is

               the 'rho' value. Note that the magnitude of these values is

               usually of the order of 10000.



               Ref:  Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30,

                     129-153.

                     Zachariasen, W. H. (1967). Acta Cryst. 23, 558-564.

                     Larson, A. C. (1967). Acta Cryst. 23, 664-665.

;

# COMMENT: This item is context sensitive in that it is necessary to know the

# _*_detail in order to interpret the coefficient.  Since there is no

# enumeration list for _*_detail, machine interpretation is impossible.  This

# item should be replaced for standard extinction methods by the following

# list of proposed items.  Can we retain the above definitioin to cover cases

# where a non-standard extinction correction was performed, or should we

# retire this name and devise a new one?

# STATUS: open for comment



data_refine_ls_extinction_coef_*

loop_    _name                  '_refine_ls_extinction_coef_Zach'

                                '_refine_ls_extinction_coef_Becker-Coppens_1'

                                '_refine_ls_extinction_coef_Becker-Coppens_2'

    _category                    refine

    _type                        numb

    _type_conditions             esd

    _example                     3472(52)

    _example_detail              'Zachariasen coefficient r* = 0.347(5) E04'

    _definition

;        The extinction coefficient used to calculate the correction

              factor applied to the structure-factor data.



         For _refine_ls_extinction_coef_Zach (the Zachariasen, also known as

              the Larson, method) the value given is the r* value,



         For _refine_ls_extinction_coef_Becker-Coppens_1 (the Becker-Coppens

              type 1 isotropic method) it is the 'g' value,



         For _refine_ls_extinction_coef_Becker-Coppens_2 (Becker-Coppens type

              2 isotropic method) it is the 'rho' value. 



         Note that the magnitude of these values is usually of the order of

              10000.



         The Becker-Coppens procedure is referred to as 'type 1' when

             correcting secondary extinction dominated by the mosaic spread;

             as 'type 2' when secondary extinction is dominated by particle

             size and includes a primary extinction component; It is also      

             possible to use a mixture of types 1 and 2.



         For the Becker-Coppens method it is necessary to set the

             mosaic distribution as either 'Gaussian' or 'Lorentzian' in       

             _refine_ls_extinction_B-C_type.  If an anisotropic extinction     

             correction has been made the multiple coefficients cannot be      

             contained in *_extinction_coef_Becker-Coppens_* and they must be

             listed in _refine_special_details.



               Ref:  Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30,

                     129-153.

                     Zachariasen, W. H. (1967). Acta Cryst. 23, 558-564.

                     Larson, A. C. (1967). Acta Cryst. 23, 664-665.

;

# COMMENT: This is a new item which allows the specific extinction parameter

# to be given for each of the standard extinction corrections.  Whichever item

# is given will identify the method used to determine the extinction so

# _*_expression and _*_method would not be needed.

# STATUS: Open for discussion.



data_refine_ls_extinction_BC_type

    _name               '_refine_ls_extinction_BC_type'

    _category            refine_ls        

    _type                        char

loop_    _related_item     

          '_refine_ls_extinction_coef_Becker-Coppens_1'

          '_refine_ls_extinction_coef_Becker-Coppens_2'

    _related_function          ?

loop_    _enumeration       Gaussian

                            Lorentzian

    _definition

;           For the Becker-Coppens extinction correction, a statement is

            needed of the function used to describe the mosaic spread. 



               Ref:  Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30,

                     129-153.

;

# COMMENT: This is a new item is needed to complement the BC coefficients

# STATUS: Open for discussion





data_refine_ls_extinction_expression

    _name                      '_refine_ls_extinction_expression'

    _category                    refine

    _type                        char

    _example

;                         Larson, A. C. (1970). "Crystallographic Computing",

                             edited by F. R. Ahmed. Eq. (22) p. 292.

                             Copenhagen: Munksgaard.

;

# A new example will be needed if the revised definition is adopted.

    _definition

;            A description or reference for the extinction correction equation

             used to apply the data item _refine_ls_extinction_coef when this

             is not one of the standard types defined under

             _refine_ls_extinction_coef_*. 

             This information must be sufficient to reproduce the extinction

             correction factors applied to the structure factors.

;

# COMMENT: The name of this item suggests an algebraic expression, but the

# example suggests that a reference is intended.  I have changed the

# definition so maybe a different dataname is needed.  It is not

# clear to me what the difference between _*_expression and _*_method was

# intended to be.

# STATUS: open for discussion.



data_refine_ls_extinction_method

    _name                      '_refine_ls_extinction_method'

    _category                    refine

    _type                        char

#    _enumeration_default        'Zachariasen'

    loop_ _example              'B-C type 2 Gaussian isotropic'

                                'none'

    _definition

;            A description of the extinction correction method applied with

             the data item _refine_ls_extinction_coef when one of the standard 

             methods is not used. 

# (The rest of this text should be deleted or transferred. The text above has

# been modified.  The enumeration default should in any case be deleted. and

# a different example given.)

#

#           This description should

#             include information about the correction method, either

#             'Becker-Coppens' or 'Zachariasen'. The latter is sometimes

#             referred to as the 'Larson' method even though it employs

#             Zachariasen's formula.

#

#             The Becker-Coppens procedure is referred to as 'type 1' when

#             correcting secondary extinction dominated by the mosaic spread;

#             as 'type 2' when secondary extinction is dominated by particle

#             size and includes a primary extinction component; and as 'mixed'

#             when there is a mixture of types 1 and 2.

#

#             For the Becker-Coppens method it is also necessary to set the

#             mosaic distribution as either 'Gaussian' or 'Lorentzian'; and

#             the nature of the extinction as 'isotropic' or 'anisotropic'.

#             Note that if either the 'mixed' or 'anisotropic' corrections

#             are applied the multiple coefficients cannot be contained in

#             *_extinction_coef and must be listed in _refine_special_details.

#

#               Ref:  Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30,

#                     129-153.

#                     Zachariasen, W. H. (1967). Acta Cryst. 23, 558-564.

#                     Larson, A. C. (1967). Acta Cryst. 23, 664-665.

;

# COMMENT: The default should be deleted since there should be no presumption

# about the method used.  This proposal changes the meaning of this item in a

# significant way and perhaps a different dataname should be used.

# STATUS: Open for comment



data_refine_ls_shift/su_max_lt

    _name                      '_refine_ls_shift/su_max_lt'

    _category                    refine

    _type                        numb

    _related_item              '_refine_ls_shift/su_max'

    _related_function            ?

    _enumeration_range           0.0:

    _definition

;              An upper limit for the largest ratio of the final

               least-squares parameter shift divided by the final 

               standard uncertainty.  This 

               item is used when the largest value of the shift 

               divided by the final standard uncertainty is too 

               small to measure.

;



data_refine_ls_shift/su_mean_lt

    _name                      '_refine_ls_shift/su_mean_lt'

    _category                    refine

    _type                        numb

    _related_item              '_refine_ls_shift/su_mean'

    _related_function            ?

    _enumeration_range           0.0:

    _definition

;              An upper limit for the average ratio of the final

               least-squares parameter shift divided by the 

               final standard uncertainty.  This

               item is used when the average value of the shift divided by 

               the final standard uncertainty is too small to measure.

;





#########################################################



# End of proposal

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