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coreCIF.dic-2.4 Discussion List #8



April 21, 2006

Dear members of the coreCIF Dictionary Maintenance Group

####################################################################
#
# PLEASE RESPOND BY 2006-05-15.  IF THIS IS INSUFFICIENT TIME LET ME
# KNOW AND I WILL EXTEND THE DEADLINE.
#
# PLEASE DO NOT BE DISCOURAGED BY THE LENGTH OF THIS MESSAGE, BUT READ
# THE INTRODUCTION FIRST.
#
####################################################################

INTRODUCTION

I apologize for the lack of activity in this discussion over the last 
few months.  This was not entirely laziness on my part.  Around the 
beginning of last summer it became clear that some important decisions 
were going to have to be made about the future directions of CIF and 
there seemed to be no points in working on details until we knew which 
way the project was headed.

The meetings held at the IUCr Congress in Florence produced a remarkable 
consensus about the future of CIF and now that we have a general idea of 
the future directions it is time to go back and finish off the 
modifications needed to the coreCIF dictionary.

First I will summarize the decisions taken in Florence as these will 
have a bearing on the work of the core Dictionary Maintenance Group. It 
was agreed that we should define a new Dictionary Definition Language, 
DDL3, based on the prototype starDDL first demonstrated by Syd Hall at 
the Glasgow IUCr Congress.  For convenience I will refer to the CIF 
dictionaries prepared with the Dictionary Definition Languages DDL1, 
DDL2 and DDL3 as CIF1 (coreCIF.dic etc.), CIF2 (mmCIF.dic etc.) and CIF3 
dictionaries respectively, and the corresponding CIFs as CIF1, CIF2 and 
CIF3.  Programs designed to work with CIF3 will be able to read all the 
archives written in CIF1 and CIF2, but they will also be able to handle 
several enhancements available in CIF3, such as the ability to define 
vectors and matrices.  CIF3 dictionaries will be based on a more 
hierarchical arrangement of categories designed to simplify the 
maintenance of the dictionaries, and they will include 'methods', i.e., 
they will be able to interpret algorithms or equations contained in the 
dictionary in order to calculate the value of an item that is not 
present in the CIF.  In effect, methods are a machine readable definition.

There is much work to be done before DDL3 is ready for launching because 
the dictionaries will have to be converted and extended, and software 
will need to be prepared.  CIF1 and CIF2 dictionaries will continue in 
use until users, convinced by the superiority of CIF3, have voluntarily 
converted.  One consequence of the hierarchical arrangement of concepts 
is that the suite of CIF dictionaries will likely be reorganized 
requiring a corresponding reorganization of the Dictionary Maintenance 
Groups.  Even though the members present in Florence wanted to see CIF3 
introduced as soon as possible, it will take a minimum of two years 
before a core dictionary and software are ready for beta testing.

Even with the new initiative the CIF1 core dictionary will be around for 
some years to come.  Therefore the core Dictionary Maintenance Group 
still has work to do.  However, some of the proposals we have been 
discussing, e.g., adding chemical information to identify molecules 
etc., will be deferred to CIF3, but in the meantime there are many 
changes that we still need to make in CIF1.  These are treated in this 
email.

Best wishes

David Brown

**********************

Proposed changes to the coreCIF1 dictionary

Earlier rounds of changes have now been incorporated in coreCIF.dic 
version 2.3, the version that appears in International Tables vol. G.  
Some items that had been approved for this version were pulled at the 
last minute as serious objections were raised.  Some of these were 
included in discussion #7, and as I received no comments on this list, 
all those items for which approval was recommended have now been moved 
to the draft coreCIF.dic version 2.4 (you will get a chance to see these 
again before we submit them to COMCIFS for final approval).

This discussion, #8, contains four sections.  Section A consists of 
items which I recommend we drop.  Section B consists of items that are 
ready for approval.  Section C contains items needing further discussion 
and Section D contains a number of miscellaneous comments.

####################################
####################################
#
#  A. ITEMS THAT PROBABLY WE CAN DROP
#
####################################
####################################
#
#  1. DIFFRN_REFLN_STATUS
#
#  2. CHEMICAL FORMULA
#
###################################
#
# These items were proposed for coreCIF.dic 2.3 but were withdrawn
# because of problems.  As the problems have not gone away
# I will drop these items unless anyone objects.
#
# RECOMMENDATION: These items be dropped.
#
####################################
#
# 1. DIFFRN_REFLN_STATUS
#
data_diffrn_refln_status
    _name               '_diffrn_refln_status'
   loop_
    _enumeration       
    _enumeration_detail
            incl        'Reflection expected to have non-zero intensity'
            sysabs      'Reflection considered to be systematically absent'
    _example                      
    _definition
;       A flag indicating whether a reflection was assumed to be
        systematically absent during the measurement of the diffraction
        intensities.
;
# COMMENT:  The purpose of this item was to allow reflection that are 
believed
# to be systematically absent to be flagged at the time they were measured.
# However as HDF points out, in order to know which reflections are
# absent one must know the space group and this is only chosen later in the
# process.  For this flag to be meaningful, a tentative space group 
would have
# to be given in the CIF, but this would be meaningless (and confusing) 
if it
# were different from the one finally adopted.  There is a way of marking
# systematically absent reflections in the refln category calculated 
after the
# structure has been solved and the space group is known.
#
########################################
#
#  2. CHEMICAL FORMULA
#
# In another discussion group Peter Murray-Rust suggested that the
# chemical_formula should indicate how the formula was obtained.  He thought
# that _chemical_formula_sum was inadequate because it does not indicate
# whether the formula was derived from the crystal structure or 
analytically.
# He suggested that we should define _chemical_formula_sum_calc and
# _chemical_formula_sum_meas.
#
# HDF writes
# ----------
# In my opinion, further discussion on this point should be pushed off 
to the
# coreDMG or coreCIFchem list.
#
# Peter has a good point with regard to _chemical_formula[] that should be
# borne in mind in relation to the work of the "group" coreCIFchem. The 
names
# need to indicate as precisely and succinctly as possible the source of the
# information.
#
# However I must say that I think that particularly bad in this respect are
# suffixes such as _meas and _calc because more or less everything we deal
# with comes from some sort of a measurement and has to be calculated to a
# greater or lesser extent. Much better are _analytical or _massspectrometry
# or _xraydiffraction.
#
# IDB comments
# ------------
# The coreCIFchem group, charged with providing a chemical description 
of the
# contents of a crystal, is currently inactive pending the introduction of
# CIF3.
# _chemical_formula_sum (and _moiety, _structural etc.) must agree
# exactly with the refined model presented in the atom_site loop. so 
they are
# determined from the structure determination.  They might
# therefore be considered to correspond to PMR's _calc or HDF's
# _xraydiffraction.  There is a _chemical_formula_analytical which is 
designed
# for information about the composition derived using a non-crystallographic
# method.  There is something to be said for adding other terms like 
_massspec
# or _xrf (x-ray fluorescence), but these could wait until there is a 
demand.
# _*_analytical is rarely used.
#
####################################




######################################
######################################
#
# B. ITEMS THAT ARE READY FOR APPROVAL
#
#--------------------------------------
#
# 3. GEOM_*_SITE_SYMMETRY           (Largely housekeeping)
#
# 4. DISTRIBUTED ELECTRON DENSITY   (Discussed earlier)
#
#
######################################
######################################
#
# These are items that have either been discussed before or are in the 
nature
# of housekeeping.  If there are no objections raised, these will be 
accepted
# for incorporation into coreCIF.dic version 2.4
#
#####################################
#
# 3. GEOM_*_SITE_SYMMETRY Revisited
# Changes to this item were approved in discussion #7 but we need to revisit
# this item.
#
#####################################
#
# EXPLANATION
# In Discussion #7 we approved splitting geom_*_site_symmetry into four 
items
# (item #1 in our approved list):
#
#                   _geom_*_site_symmetry_symop
#                   _geom_*_site_symmetry_trans_a
#                   _geom_*_site_symmetry_trans_b
#                   _geom_*_site_symmetry_trans_c
#
# The reason for this change was so as not to limit the distance over 
which a
# symmetry-related atom could be addressed.  However, since the vector 
format
# in DDL3 provides a more elegant solution to this problem which in any
# case is not of high priority, it is best to leave this to CIF3.
# Therefore our earlier approval of these items should be withdrawn
#
# There is, however, a more immediate problem we need to address.
#
# In the first version of the core dictionary default values were introduced
# for a number of items, but some of these made little sense, e.g., a 
default
# of 0 for h, k and l.  We have gradually been removing these meaningless
# defaults, but in the case of _geom_*_site_symmetry a default has 
always been
# assumed (on the basis of an example given in dictionary) even though no
# default is given in the dictionary definition.
# Most currently generated CIFs use a period to
# indicate that this item defaults to 1_555, i.e., the coordinates given in
# the atom_site list are not transformed. In the proposed change this 
default
# is made explicit.
#
# Related to this is the fact that there is currently no requirement in the
# dictionary that symop 1 be the identity operation. 
# We therefore need to add a note to the definitions of several items
# that the _*_id value of the identity operation should
# be 1.
#
#
#
# PROPOSAL
# 1. Drop the recently approved items
#                   _geom_*_site_symmetry_symop
#                   _geom_*_site_symmetry_trans_a
#                   _geom_*_site_symmetry_trans_b
#                   _geom_*_site_symmetry_trans_c
#
# 2. Add to _space_group_symop_id and _symmetry_equiv_pos_site_id
#                   _enumeration_default 1
#
# 3. Add to _symmetry_equiv_pos_as_xyz
#                   _enumeration_default x,y,z
#
# 4. Add the following sentence to the definitions of
# _space_group_symop_operation_xyz, _space_group_symop_id,
# _symmetry_equiv_pos_as_xyz and _symmetry_equiv_pos_site_id:
#
#;                   In order for the defaults to work correctly, the 
identity
#                    operation should have _space_group_symop_id or
#                    _symmetry_equiv_pos_site_id set to 1, and
#                    _space_group_symop_operation_xyz or
#                    _symmetry_equiv_pos_as_xyz set to x,y,z,
#                    i.e., the operation labelled 1 should be the identity
#                    operation.
#;
#
# RECOMMENDATION: That this item be approved.
#
####################################
#
#  4. DISTRIBUTED ATOMIC DENSITY                Ready for approval
#
#####################################
#
# STATUS: Ready for approval
#
# RECOMMENDATION:  The following items be approved
#
# INTRODUCTION
#
# The following items which were included in the previous discussion are 
based
# on a request from David Watkin.
# They are intended to describe atoms that are disordered or moving so that
# their atomic density is assumed to be distributed over a simple geometric
# shape such as a ring as might arise from a rotating group such as a
# trifluooromethyl group or a cyclopentadiene molecule. 
#
# Various possible shapes are defined - ring, spherical shell,
# cylindrical shell, etc.  The atoms that form the ring or shell are listed
# with dummy coordinates in the atom_site loop.  This is necessary to allow
# the composition of the crystal to be calculated. 
# The dummy atoms are flagged with an identifier
# that links them to a new category giving details of the shape of the
# distribution, thus allowing, e.g., the scattering density to be 
calculated.
# This requires the introduction of an _atom_site_distributed_density_id 
item
# in the atom_site category, and the definition of a new distributed_density
# category.
#
# David Watkins is currently adapting CRYSTALS to provide a CIF output for
# distributed density and for this purpose he is defining a few extra local
# 'Oxford' datanames: specifically an _atom_site_occupancy that may take
# values greater than 1.0 (not permitted in _atom_site_occupancy) and 
items to
# define the directions of lines, rings, etc. in terms of Euler angles based
# on the choice of orthogonal axes assumed by CRYSTALS.  The method of
# defining the direction (based on reciprocal space coordinates) given 
here is
# independent of any arbitrary convention.
#
# I apologize for the length of this item, but we have seem it all before.
#
#################
#
# A new item for the ATOM_SITE category
#
#################
#
data__atom_site_distributed_density_id
    _name               '_atom_site_distributed_density_id'
    _category           atom_site
    _type               char
    _list               yes
    _list_reference     '_atom_site_label'
    _list_mandatory     no
    _link_parent        '_distributed_density_id'
    _example            ?
    _definition
;              An identifier that links the atom defined by _atom_site_label
               with the distributed density of this atom defined in the
               distributed_density category. 
               Note that all the atoms that give rise to a particular
               distributed density, e.g., a ring, should be included in the
               atom_site list, even when they, or the centroid of the
               distribution, lie on a special position.
               That is, the crystallographic site symmetry of the 
distribution
               is not used to
               generate the full distributed density shape from the
               crystallographic asymmetric portion.
               The value of _atom_site_symmetry_multiplicity should be 
chosen
               so that for each of the atoms in the atom_site list
               _atom_site_occupancy multiplied by
               _atom_site_symmetry_multiplicity is equal to its contribution
               to the _chemical_formula_sum multiplied by
               _cell_formula_units_Z.
;
#
#
##########################
#
#   New Category  DISTRIBUTED DENSITY
#
##########################
#
data_distributed_density_[]
    _name               '_distributed_density_[]'
    _category           category_overview
    _type               null
    _definition
;              Items in the distributed_density category describe the
               geometric arrangement of an atom or atoms when they are
               distributed uniformly over a line or surface such as a ring,
               cylindrical shell or spherical shell, the line or surface 
being
               given a thickness through the application of an atomic
               displacement parameter.
;
loop_     _example_detail
          _example
;
This example is fictitious (and chemically implausible) but it is 
designed to illustrate how a complex system of distributed density can 
be recorded.  In this example pentamethyl cyclopentadiene (Cp*) and 
borazole occupy the same location in the crystal in the ratio 5:1.  The 
atoms of the borazole ring are fixed as are three quarters of the atoms 
in the Cp* ring, but the remaining quarter of the Cp* molecules are 
freely rotating around the cylindrical Cp* axis.  The rotating Cp* 
molecules give rise to two concentric rings of density, one from the 
atoms in the ring and the other from the methyl groups (hydrogen atoms 
are ignored).  On top of these rings lie the atoms of the fixed Cp* 
molecules.  The atoms of the borazole molecule also lie over the inner 
Cp* ring.  Full details of the chemical composition are given in the 
atom_site loop together with the positions of the fixed atoms.
The coordinates of the atoms that give rise to the distributed ring of 
density are set to '.', meaning that they have no significance as the 
atoms are dummy atoms included to give the correct composition providing 
that _atom_site_occupancy and _atom_site_symmetry_multiplicity are given. 
The composition defined in the atom_site loop is linked to the
distributed_density loop through the parent-child identifiers, 'an1' and 
'an2' (for annulus 1 and 2). 
The one quarter of the Cp* molecules that are rotating have the occupation
number of 0.208 = 5/6 (the total occupancy of the Cp*)  x 1/4 (the portion
rotating) = 5/24.  The three quarters that are in fixed positions have 
the occupation number of 0.625 = 5/6 x 3/4 = 15/24 .
;
;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_occupancy
  _atom_site_symmetry_multiplicity
  _atom_site_adp_type
  _atom_site_distributed_density_id
  _atom_site_calc_flag
#
# Inner ring of cyclopentadiene carbon atoms and borazole
C1   C -0.1362(8)  -0.0974(8)  -0.3116(10) 0.0662(18) 0.625(1) 4  Uiso . d
C2   C -0.1060(8)  -0.2165(8)  -0.1837(10) 0.071(2)   0.625(1) 4  Uiso . d
C3   C -0.1774(9)  -0.1939(9)  -0.0820(11) 0.082(2)   0.625(1) 4  Uiso . d
C4   C -0.2529(9)  -0.0561(9)  -0.1479(12) 0.084(2)   0.625(1) 4  Uiso . d
C5   C -0.2261(8)  -0.0002(8)  -0.2891(10) 0.072(2)   0.625(1) 4  Uiso . d
C1a  C   .           .           .          .         0.208(1) 4   .  
an1 dum
C2a  C   .           .           .          .         0.208(1) 4   .  
an1 dum
C3a  C   .           .           .          .         0.208(1) 4   .  
an1 dum
C4a  C   .           .           .          .         0.208(1) 4   .  
an1 dum
C5a  C   .           .           .          .         0.208(1) 4   .  
an1 dum
N1   N -0.1375(8)  -0.0968(8)  -0.3201(10) 0.065(2)   0.167(1) 4   Usso . d
B1   B -0.1002(8)  -0.2265(8)  -0.1728(10) 0.071(2)   0.167(1) 4   Uiso . d
N2   N -0.1402(8)  -0.1034(8)  -0.0765(10) 0.076(2)   0.167(1) 4   Uiso . d
B2   B -0.2370(9)  -0.0364(9)  -0.1832(10) 0.085(2)   0.167(1) 4   Uiso . d
N3   N -0.2893(8)   0.0034(8)  -0.3621(10) 0.062(2)   0.167(1) 4   Uiso . d
B3   B -0.2246(9)  -0.0452(9)  -0.3004(11) 0.073(2)   0.167(1) 4   Uiso . d
# Outer ring of methyl groups
C11  C -0.0951     -0.0733     -0.4330     0.1901     0.625(1) 4   Uani . d
C12  C -0.0272     -0.3236     -0.1750     0.1990     0.625(1) 4   Uani . d
C13  C -0.1719     -0.2833      0.0404     0.2483     0.625(1) 4   Uani . d
C14  C -0.3291     -0.0080     -0.0844     0.2450     0.625(1) 4   Uani . d
C15  C -0.2817      0.1218     -0.3770     0.2219     0.625(1) 4   Uani . d
C11a C   .           .           .          .         0.208(1) 4   .  
an2 dum
C12a C   .           .           .          .         0.208(1) 4   .  
an2 dum
C13a C   .           .           .          .         0.208(1) 4   .  
an2 dum
C14a C   .           .           .          .         0.208(1) 4   .  
an2 dum
C15a C   .           .           .          .         0.208(1) 4   .  
an2 dum
# Details of the two rings of distributed density are given in the following
# loop.
loop_
  _distributed_density_id
  _distributed_density_shape
  _distributed_density_position_x
  _distributed_density_position_y
  _distributed_density_position_z
  _distributed_density_radius
  _distributed_density_direction_h
  _distributed_density_direction_k
  _distributed_density_direction_l
  _distributed_density_Uiso
  _distributed_density_symmetry_multiplicity
an1 ring -0.1810(8)  -0.1133(8)  -0.2058(8)   
                1.198(6)    1.35(2) 0.07(2) -0.45(2)   0.052(2)   4
an2 ring -0.1873(14) -0.1156(14) -0.2210(2)
                2.626(6)    1.30(2) 0.10(2) -0.40(2)   0.131(3)   4
;

data_distributed_density_details
    _name             '_distributed_density_details'
    _category          distributed_density
    _type              char
    _list              both
    _list_reference    '_distributed_density_id'
    _example           
;              The distribution was modelled using a disk of
               density of the given radius.
;
    _definition
;              Information about the distribution of density not
               given in other items.
;

data_distributed_density_direction_
loop_    _name              
                      '_distributed_density_direction_h'
                      '_distributed_density_direction_k'
                      '_distributed_density_direction_l'
    _category         distributed_density
    _type             numb
    _type_conditions  esd
    _list             both
    _list_reference   '_distributed_density_id'
    _units            rlu
    _units_detail     reciprocal lattice units
    _example          ?
    _definition
;      The (covariant) components on a reciprocal-lattice basis of a 
vector of
       arbitrary length used to indicate the direction of the unique axis of
       the distribution, e.g., the axis of a cylindrical shell or the normal
       to the plane of a ring.
;

data__distributed_density_id
    _name             '_distributed_density_id'
    _category         distributed_density
    _type             char 
    _list             both
    _list_reference   '_distributed_density_id'
    _list_mandatory   yes
    _link_child       '_atom_site_distributed_density_id'
    _example          ?
    _definition       An identifier that links the atom defined by
                      _atom_site_label with a distributed density defined in
                      the distributed_density category.        
;
#
data__distributed_density_length
    _name             '_distributed_density_length'
    _category         distributed_density
    _type             numb
    _type_conditions  esd
    _list             both
    _list_reference   '_distributed_density_id'
    _enumeration_range 0.0:
    _units            A
    _units_detail     Angstrom units
    _example          ?
    _definition
;              The length of the line or cylindrical shell of distributed
               density in Angstrom units.
;
#
data__distributed_density_position_
loop_    _name              
                      '_distributed_density_position_x'
                      '_distributed_density_position_y'
                      '_distributed_density_position_z'
    _category         distributed_density
    _type             numb
    _type_conditions  esd
    _list             both
    _list_reference   '_distributed_density_id'
    _example          ?
    _definition
;              The position of the centroid of the distributed density in
               fractions of the unit cell values.
;
#
data__distributed_density_radius
    _name             '_distributed_density_radius'
    _category         distributed_density
    _type             numb
    _type_conditions  esd
    _list             both
    _list_reference   '_distributed_density_id'
    _enumeration_range 0.0:
    _units            A
    _units_detail     Angstrom units
    _example          ?
    _definition
;              The radius of the ring, or of the cylindrical or spherical
               shell, of distributed density in Angstrom units.
;
#
data__distributed_density_shape
    _name             '_distributed_density_shape'
    _category         'distributed_density
    _type             char
    _list             both
    _list_reference   '_distributed_density_id'
loop_   
  _enumeration
  _enumeration_detals
      line            'line segment'
      infline         'an infinite line running through the crystal'
      ring            'a circular ring'
      cylshell        'cylindrical shell of finite length'
      infcylshell     'cylindrical shell running through the crystal'
      sphereshell     'spherical shell'
      other           'Give details in _distributed_density_details'
    _definition
;              A flag that indicates the shape of the distributed density.
               The lines and ring are one dimensional distributions of
               atoms and the cylindrical shell and spherical shell are two
               dimensional distributions. 
               In each case the root-mean-square thickness of the 
distribution
               is given by the atomic displacement parameter defined in
               _distributed_density_Uiso.
;
data__distributed_density_symmetry_multiplicity
    _name             '_distributed_density_symmetry_multiplicity'
    _category         distributed_density  
    _type             numb
    _list             both
    _list_reference   '_distributed_density_id'
    _enumeration_range 1:192
    _example          ?
    _definition
;              The number of images of the centroid of the distributed 
density
               that the space group symmetry generates in the unit cell
               reported in the cell category.  It is the number that
               appears in International Tables for Crystallography Vol A for
               the Wyckoff position occupied by the centroid.

               In this treatment the symmetry of the distribution itself is
               ignored, including any operations of its point group that are
               part of the crystallographic site symmetry of the 
centroid.    
               All the atoms that give rise to the distributed density 
should
               therefore be listed in the atom_site category even if 
they, or
               the centroid of the distribution, lie on crystallographic
               special positions.
               E.g., if the distribution is a ring and the centroid of the
               ring lies on a crystallographic mirror plane, all the 
atoms in
               ring are listed if the ring lies either in or 
perpendicular to
               the mirror plane since the mirror image of the ring lies over
               the ring itself. 
               If the ring is at some arbitrary angle to the mirror 
plane, the
               mirror generates a second ring and both rings should be
               described independently. 
               However, because both rings cannot be simultaneously 
occupied,
               the occupation numbers given in the atom_site category must
               have a value equal to or less than 0.5.
;
#
data__distributed_density_Uiso
    _name                '_distributed_density_Uiso'
    _category            distributed_density       
    _type                numb
    _type_conditions     esd
    _list                both
    _list_reference      '_distributed_density_id'
    _enumeration_range   0.0:
    _units               A^2^
    _units_detail        'Angstrom units squared'
    _example             0.018(3)
    _definition
;              The factor exp(-Ux^-2^)is applied to all parts of the 
distribution, where U = _distributed_density_uiso and x is the distance 
from the ideal 1- or 2- dimensional shape.  This emulates the effects of 
thermal motion or static displacement from the ideal positions described 
in this category and has the effect of converting the simple 1- or 
2-dimensional geometric shapes into 3-dimensional objects of mean square 
thickness U.
;
#

########################################
########################################
#
#  C. ITEMS REQUIRING FURTHER DISCUSSION
#
########################################
########################################
#
#  5. GEOM_BOND                                 Open for discussion
#
#  6. _EXPTL_ABSORPT_CORRECTION_T_max and T_min Open for discussion
#
#  7. REFINE_ELECTRON_DENSITY                   Open for discussion
#
#  8.  _ATOM_SITE_REFINMENT_FLAG_ADP            Open for discussion
#
#  9.  _ATOM_SITES_SOLUTION_*                   Open for discussion
#
#  10. _CHEMICAL_ENANTIOEXCESS_BULK_*           Open for discussion
#
#  11. _PUBL_SECTION_KEYWORDS                Open for discussion
#
#  12. DIMENSIONLESS UNITS                      Open for discussion
#
##########################################
#
#  5. GEOM_BOND
#
##########################################
#
# COMMENT: In high symmetry structures when many bonds are related by 
symmetry
# it is not necessary to list all the bonds in the environment of the first
# named atom.  Some users may wish to give only the symmetry independent
# distances and a multiplier to indicate how many such bonds are found 
in the
# atomic environment.
#
data_geom_bond_multiplicity
    _name               '_geom_bond_multiplicity'
    _category            geom_bond       
    _type                numb       
    _type_conditions            
    _list                yes       
    _list_reference      '_geom_bond_atom_site_label_'   
    _enumeration_range   0:
    _definition
;       The number of times the given bond appears in the environment of
        the atoms labelled _geom_bond_atom_site_label_1.          
;
# STATUS: Open for discussion

###########################################
#
# 6. EXPTL_ABSORPT_CORRECTION_T_max and T_min
#
###########################################
#
# The current definition of these items is:
#
#     The maximum and minimum transmission factors for the crystal
#     and radiation. These factors are also referred to as the
#     absorption correction A or 1/A*.
#
# but there have been a variety of different interpretations as to what this
# means, viz:
#
# 1.  These values are the transmission factors that were used in correcting
# the diffraction intensities for absorption. (Acta Cryst. has adopted this
# interpretation.)
#
# 2. These are the true transmission factors, whether or not any correction
# was made for absorption.  They are shown to give an indication of the
# importance of absorption in this specimen.
#
# 3. These corrections apply to the crystal alone and not the specimen mount
# (e.g., the capillary).
#
# 4. These corrections apply to the crystal and specimen mount (including
# mother liquor and container).  In some experiments (e.g., in a diamond 
anvil
# high pressure experiment) the container may absorb more strongly than the
# specimen.
#
# And how should these be interpreted in the case of multiple wavelengths
# where the transmission factors are not constant?
#
# These uncertainties should be resolved.  Maybe we need more than one 
set of
# transmission factors.  Your suggestions would be welcome.
#
# Relevant to this discussion are comment received from Ross Angel who is
# is writing a program for reporting high-pressure results as CIF.
#
# RA writes:
# ----------
# The most important issues with respect to high-pressure data concern data
# corrections and how to describe them in the cif.  At least the  following
# issues would need to be addressed:
#
# 1) A flag to tell cif checkers that completeness is not expected 
because of
# restrictions by the sample conditioning device.
#
# 2) Definition of whether the terms _exptl_absorpt_correction_T_max and 
T_min
# apply to the total correction to an intensity, or just the correction from
# the crystal.
#
# 3) A way to document the corrections for the absorption and shadowing 
by the
# pressure cell
#
# 4) A way to describe the crystal faces in an x-y-z coordinate system 
instead
# of hkl and d. The crystal faces approach is not appropriate for many
# high-pressure devices.
#
# The problem with items 3 and 4 is that they will differ from one lab to
# another. What I have done is to put all of this information into
# "_exptl_absorpt_process_details" and "_exptl_crystal_description " as
# follows:
#
_exptl_absorpt_process_details
;
Gaussian integration over a grid
of 16 x  8 x 16 points =  2048 total grid points
   Based upon method of Burnham (1966)

  Data corrected for diamond-anvil cell absorption
  Note that exptl_absorpt_correction_tmin and _tmax
  the total correction factors applied to the intensities
  The individual factors are:
      range of dac transmission factors (min-max)      0.703     
0.980        
      range of gasket transmission (min-max)           0.992     
1.000        
      range of P media transmission (min-max)          1.000     1.000 
DAC transmission function with sum(mu*t) for anvil 1:  0.607  anvil  2:  
0.607

     Gasket shadowing corrections were made based upon
     Gasket thickness = 114.0 microns, radius = 140.0 microns     
     Gasket absorption coeff =        30.00 mm-1
     REFLECTION WAS CONSIDERED TOTALLY OBSCURED IF
  FRACTION CRYSTAL ILLUMINATED WAS LESS THAN 0.20

     Non-absorbing pressure medium
;
_exptl_crystal_preparation      'mounted in a diamond-anvil cell ' 
_exptl_crystal_description
;
  crystal was described in terms of coordinates of corners on the 
orthogonal phi-axis coordinate system of Busing and Levy (1967) (i.e., 
+Y along beam, +Z up at circles zero, +X to make right-handed set)   
with origin at the centre of the face of the incident-beam anvil    loop 
is over x, y, z (mm)
   -0.044000    0.000000    0.061000
    0.073000    0.000000    0.032000
   -0.069000    0.000000   -0.032000
    0.048000    0.000000   -0.060000
   -0.044000    0.060000    0.061000
    0.073000    0.060000    0.032000
   -0.069000    0.060000   -0.032000
    0.048000    0.060000   -0.060000
;
#
# [IDB: See the note in Section D below regarding choice of axis systems in
# CIF.  The choice adopted here is different.]
#
# STATUS: Open for discussion.
#

##########################################
#
#  7. REFINE_ELECTRON_DENSITY
#
##########################################
#
# COMMENT: The following items form a new category giving a list of peaks
# in the electron density. 
# This has been requested by a user as a useful adjunct to the other refine
# items.
#
# This does, however, raise the question of whether there might be a greater
# need for other peak functions such as peaks in the Patterson function 
or in
# the difference electron density. 
#
# Without any further information supplied elsewhere by the user,
# one would assume that these peaks are those found in the final electron
# density map, but the examples given below suggest that it might be a 
density
# map produced much earlier in the structure determination process.
# Since the final structure is fully described by the list of occupied
# atom_sites, it is not clear that knowing the positions and heights of the
# peaks in the final electron density map is of much value except in the 
rare
# case where a number of peaks do not occur at atom sites. 
#
# Is the name correct or should we use a more general name
# such as _refine_scattering_density?  If this is generalized to include
# neutron diffraction results, _*_peak might presumably be negative.
#
data_refine_electron_density_[]
    _name               refine_electron_density
    _category           null
    _type               category_overview        
    _example 
;   loop_
       _refine_electron_density_id
       _refine_electron_density_position_x
       _refine_electron_density_position_y
       _refine_electron_density_position_z
       _refine_electron_density_peak
       _refine_electron_density_details
  1   0.0743   0.3568   0.4215  45.6     'probably Mo'
  2   0.7358   0.2987   0.8932  43.2     'probably Mo'
  3   0.8657   0.4518  -0.0654  25.8       ?
;
    _definition
;              This is a category in which the peak positions and heights in
               the experimental electron density map can be reported.
;
# STATUS: Open for discussion

data_refine_electron_density_details
    _name               '_refine_electron_density_details'
    _category           refine_electron_density       
    _type               char        
    _list               yes
    _list_reference     '_refine_electron_density_details   
   loop_    _example     'Probably Mo'
                         'Uncertain peak'
                         'Broad diffuse peak'
    _definition
;              A description of the electron density peak
;

data_refine_electron_density_id
    _name               '_refine_electron_density_id'
    _category           refine_electron_density
    _type               char        
    _list               yes
    _example                       ?
    _definition
;              A code identifying this particular electron density peak
;

data_refine_electron_density_peak
    _name               '_refine_electron_density_peak'
    _category           refine_electron_density
    _type               numb  
    _list               yes
    _list_reference     '_refine_electron_density_id'
    _units              e.A-3
    _units_detail       'electrons per cubic angstrom'
    _example                       ?
    _definition
;              The measured electron density at the given peak position.
;

data_refine_electron_density_position_
 loop_
   _name               _refine_electron_density_position_x
                       _refine_electron_density_position_y
                       _refine_electron_density_position_z
   
    _category          refine_electron_density             
    _type              char
    _list              yes
    _list_reference    _refine_electron_density_id       
    _example                       ?
    _definition
;              The positional coordinates in fractions of the unit cell at
               which the electron density peak occurs.
;
# STATUS: Open for discussion
#

########################################
#
#   8.  _ATOM_SITE_REFINMENT_FLAG_ADP
#
########################################
#
# Curt Haltiwanger suggests that we need to extend the enumeration list for
# this item.  He writes:
#
# There are at least three common restraints for adp's
#
# 1.  'rigid bond' [SHELXL - DELU] restraint  -  i.e. the components of the
# adp in the direction of the bond are restrained to have similar numerical
# values
#
# 2.  'near neighbor' (My term) [SHELXL - SIMU] restraint  -  Atoms closer
# than a specified distance are restrained to have the same Uij components.
#
# 3.  'approximate isotropic' (My term) [SHELXL - ISOR] restraint  -  atoms
# are restrained so that their Uij components approximate to isotropic
# behavior
#
# The enumeration detail should reflect these possibilities and those in 
other
# refinement packages. 
#
# In addition, SHELXL can has the provision for several atoms to have 
exactly
# the same adp's or some multiplier times the adp.  These would also be a
# candidate for enumeration.   I have no knowledge of the restraints and
# constraints used in other programs.
#
# [IDB: COMMENT: There is confusion between the meaning of 'constraint' and
# 'restraint'.  A 'constrained parameter' is one that is not refined.  
It may
# be reset between refinements, e.g., to be equal to one of the refined
# parameters, and so may change as the refinement progresses, but it is 
not a
# variable in the least squares calculation.  A 'restraint' is a target 
value
# for some structure dependent variable (not one that is being
# refined) that is added to the target list of observed structure 
factors and
# is treated as an observation, suitably weighted.  I believe that Curt is
# referring here to constraints, not restraints.
#
# The list of flags in the current dictionary is:
#
#         .  No constraints
#         T  Special position constraints on ADPs
#         U  Uiso or Uij restraint (sic) (rigid bond)
#         TU Both constraints applied.]
#
# CH continues:
# So
# S   'special-position constraints on atomic displacement parameters'
#            [this should be T, IDB]
# R
#;     adp in the direction of connecting bond are restrained to similar
#             (rigid bond)
#;
# N   'adp of nearby atoms are restrained to have similar Uij's
# I   'adp restrained to approximate isotropic behavior'
# E   'adp exactly tied to adp of another atom'
# M   'adp based on multiplication factor of the adp of another atom'
# SR   'combination of the above constraints'  
# SN   'combination of the above constraints'  
# SI   'combination of the above constraints'  
# SE   'combination of the above constraints'  
#         etc   
#
# Alternatively remove rigid bond from the definition
# U  'Uiso or Uij restraint'
# or add other possibilities
# U  'Uiso or Uij restraint ( rigid bond, approximate isotropic, tied 
)'        #
# [IDB: Do we really need to go into this amount of detail?  Someone is sure
# to find another kind of constraint that can be applied.  I recommend 
that we
# follow CH's last suggestion and redefine U as:
#
# U  
# ;Uiso or Uij as constrained to a value determined by neighbouring or 
related
# atoms
# ;
#
# STATUS: Open for discussion
#

#######################################
#
#  9.  _ATOM_SITES_SOLUTION_*
#
#######################################
#
# COMMENT: Bruce Noll has suggested (2005-02-22) that the enumeration list
# needs updating to include 'other' in addition to at least Sheldrick's Dual
# Space method.  This would require the following additions to the 
enumeration
# list of _atom_sites_solution_*

  loop_  _enumeration  _enumeration_detail
         dual        'Sheldrick's dual space method (***reference 
needed***)'
         other         'a method not included elsewhere in this list'
#
# STATUS: Open for discussion
#

#######################################
#
# 10. _CHEMICAL_ENANTIOEXCESS_BULK_*
#
#######################################
#
# HDF (05-07-25) suggests the need for the following item
#
data_chemical_enantioexcess_bulk
    _name                      '_chemical_enantioexcess_bulk'
    _category                    chemical
    _type                        numb
    _type_conditions             esd
    _enumeration_range           0.0:1.0
    _units                       U
# See the note on units in Section D below
    _units_detail                dimensionless
    _definition
;              The enantioexcess of the bulk material from which the
               crystals were grown.
               A value of 0.0 indicates the racemate. A value of 1.0
               indicates that the compound is enantiomerically pure.
               Enantioexcess is defined in the IUPAC Recommendations
               1996, Basic Terminology of Stereochemistry, Moss G.P. (1996)
               Pure and Applied Chemistry, 68, 2193-2222, available at
               http://www.chem.qmul.ac.uk/iupac/stereo/index.html
;


data_chemical_enantioexcess_bulk_technique
    _name                      '_chemical_enantioexcess_bulk_technique'
    _category                    chemical
    _type                        char
    loop_ _enumeration
          _enumeration_detail    OA
;                                     enantioexcess determined by
                                      measurement of the specific rotation
                                      of the optical activity of the bulk
                                      compound in solution
;
                                 CD
;                                     enantioexcess determined by
                                      measurement of the visible/near UV
                                      circular dichroism spectrum of the
                                      bulk compound in solution
;
                                 EC
;                                     enantioexcess determined by
                                      enantioselective chromatography of
                                      the bulk compound in solution
;
    _definition
;              The experimental technique used to determine the
               enantioexcess of the bulk compound.
;

data_chemical_enantioexcess_crystal
    _name                      '_chemical_enantioexcess_crystal'
    _category                    chemical
    _type                        numb
    _type_conditions             esd
    _enumeration_range           0.0:1.0
    _units                       U
# See the note on units in Section D below
    _units_detail                dimensionless
    _definition
;              The enantioexcess of the crystal used for the diffraction
               study. A value of 0.0 indicates the racemate. A value of
               1.0 indicates that the crystal is enantiomerically pure.
               Enantioexcess is defined in the IUPAC Recommendations
               1996, Basic Terminology of Stereochemistry, Moss G.P. (1996)
               Pure and Applied Chemistry, 68, 2193-2222, available at
               http://www.chem.qmul.ac.uk/iupac/stereo/index.html
;


data_chemical_enantioexcess_crystal_technique
    _name                      '_chemical_enantioexcess_crystal_technique'
    _category                    chemical
    _type                        char
    loop_ _enumeration
          _enumeration_detail    CD
;                                     enantioexcess determined by
                                      measurement of the visible/near UV
                                      circular dichroism spectrum of the
                                      crystal taken into solution
;
                                 EC
;                                     enantioexcess determined by
                                      enantioselective chromatography of
                                      the crystal taken into solution
;
    _definition
;              The experimental technique used to determine the
               enantioexcess of the crystal.
;
#
# STATUS: Open for discussion
#

#################################
#
#  11. _PUBL_SECTION_KEYWORDS
#
#################################
#
# Doug Boulay (05-06-25):
# After reading David's report,
# I notice the the current CIF dictionaries
# don't seem to have any explicit publication specific keyword
# metadata definitions, such as
#
#      _publ_manuscript_keywords
# or
#      _publ_section_keywords
#
# Probably just an oversight considering the wealth of
# other _publ_ and _journal_ definitions therein.
# But it could be quite useful for propagating into
# Dublin-core (RDF) subject metadata for HTML and XML
# renderings of CIF. It would probably need an official vocabulary of
# terms and terminology to do it rigorously though.
#
# mmCIF does have these definitions:
#
# _entity_keywords.text
# _struct_keywords.text
# _struct_biol_keywords.text
# _struct_site_keywords.text
#
# [IDB: These items do not have an enumeration list]
#
data_publ_section_keywords
    _name               '_publ_section_keywords'
    _category           publ        
    _type               char        
    _list               yes
    _list_reference     '_publ_section_keywords_id'      
    _example                       ?
    _definition
;              Keywords associated with the manuscript
;
data_publ_section_keywords_id
    _name               '_publ_section_keywords_id'
    _category            publ
    _type                char       
    _list                yes
    _list_mandatory      yes           
    _example                       ?
    _definition
;              A unique identifier for a keyword in a list.
;
#
# STATUS: Open for discussion
#

########################
#
# 12. DIMENSIONLESS UNITS
#
# COMMENT: HDF provides the following information
#
# 24.1 Interdivisional Committee on Terminology, Nomenclature and Symbols of
# the International Union of Pure and Applied Chemistry (IUPAC ICTNS)
#
# Another proposal concerns the use of the name 'uno', symbol U, for the 
unit
# one so that dimensionless numbers may be treated in the same way as all
# other SI units.
# Thus, a second phase in a material detected at a 15 \mg/kg level, for
# example, would be expressed as 15 nU (15 nanouno) of that phase.
# Among other advantages, the proposed unit eliminates the present 
widespread
# and sometimes ambiguous use of abbreviations such as ppm (for the number
# 10^-6^), ppb (for the number 10^-9^ in the USA and UK, 10^-12^ in
# continental Europe).
# CCU had proposed the name uno in 1999 but no action was taken at that time
# by the Comité International des Poids et Mesures.
# All Directors of National Institutes of Metrology and other relevant
# institutions have been canvassed for the widest views on the proposal.
#
# [IDB: adding uno to the list of units would result in the following item.]
#
 data_units
     _definition
;              A unique code which identifies the units of the defined data
                item. A description of the units is provided in 
_units_detail.
;
     _name                      '_units'
     _category                    units
     _type                        char
     loop_ _example
           _example_detail         K    'kelvins'
                                   C    'degrees Celsius'
                                   rad  'radians'
                                   e    'electrons'
                                   V    'volts'
                                   Dal  'daltons'
                                   m    'metres'
                                   kg   'kilograms'
                                   s    'seconds'
                                   U    'uno (dimensionless units)'
#
# STATUS: Open for discussion
#
################################



################################
#
# D. OTHER OUTSTANDING ITEMS
#
################################
#
#  TWINS
#
# Simon Parsons, Vic Young and colleagues are working on a description of
# twinning. 
# Their proposal is not yet ready to bring to the DMG.
#
#  DETAILS OF SCANS FOR INDIVIDUAL REFLECTIONS
#
# (angles, ranges etc.) Suggested by Curt Haltiwanger. 
# They will require a new category diffrn_refln_scan.
# Curt is currently preparing definitions.
#
# TREATMENT OF STANDARD UNCERTAINTY
#
# Some items that occur with standard uncertainties have enumeration ranges
# that are determined by physical limitations.
# For example, an occupation number cannot physically be greater than 1.0 or
# less than zero.
# However, experimentally measured values may be as much as 3*sigma less 
than
# zero or 3*sigma greater than 1.0.
# At present there is no way in which information on the correct
# treatment of enumeration ranges for experimentally determined 
quantities is
# coded in a machine readable (or any other) form.
# Does anyone have any suggestions?
#
# MACHINE-INDEPENDENT AXES
#
# Ross Angel suggests that in high pressure work it is better to 
describe the
# crystal shape in a diffractometer-based Cartesian coordinate system rather
# than a reciprocal-cell based system.
# The conversion between these is related to the orientation matrix of the
# crystal but the present definition of this matrix is unsatisfactory 
because
# it depends on the design of the diffractometer.
# Recently a unique definition of a Cartesian coordinate system that 
does not
# involve the direction of gravity (up-down) has been prepared for the 
imgCIF
# dictionary.
# This should become the standard for all CIFs and should appear 
somewhere in
# the core. 
#
# The convention is given in the introduction to the AXIS category in imgCIF
# and can be summarized as follows:
#
# The ORIGIN is chosen at the centre of the specimen.
# The X axis is aligned to the principal mechanical axis of the goniometer
# This is the axis of the circle furthest removed from the specimen; it is
# usually fixed in the laboratory space and is frequently vertical or
# horizontal.
# The Y axis is perpendicular to the plane defined by the X axis and the
# incident beam, maintaining a right-handed system with X and Z.
# The Z axis is perpendicular to X and Y and its positive direction is 
on the
# same side of the XY plane as the radiation source.
# Any axis system can be defined in terms of these vectors and an origin
# shift vector (in mm) from the specimen.
#
#########################################################

# The following is a template that can be used for new definitions
data_
    _name              
    _category                   
    _type                       
    _type_conditions            
    _list                       
    _list_reference           
    _list_mandatory
    _related_item             
    _related_function         
    _enumeration_range
    _units                    
    _units_detail             
    _example                      
    _definition
;             
;
# COMMENT:
# STATUS:
begin:vcard
fn:I.David Brown
n:Brown;I.David
org:McMaster University;Brockhouse Institute for Materials Research
adr:;;King St. W;Hamilton;Ontario;L8S 4M1;Canada
email;internet:idbrown@mcmaster.ca
title:Professor Emeritus
tel;work:+905 525 9140 x 24710
tel;fax:+905 521 2773
version:2.1
end:vcard

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