CORECIF DISCUSSION PAPER # 9

Dear Colleagues,

Please respond to this discussion list by January 15, 2007.  If you need longer time, let me know and I will arrange to extend the deadline.  We are getting close to the end of the items we need to consider for this round of revisions.

A number of comments received on Discussion Paper #8 are repeated or summarized below. 

This Discussion Paper is divided into two sections.  Section A deals with a number of general matters.  Section B makes recommendations for specific items. I look forward to your comments on these matters, but as always, I will assume that no comment means that you agree with the recommendations given below.

****************************************************
*
*  A. GENERAL ITEMS
*  ----------------
*  A1 CHEMICAL INFORMATION
*
*  A2 REPORTING CONSTRAINTS AND RESTRAINTS
*
****************************************************

A1 CHEMICAL INFORMATION
----------------------

Howard Flack writes: 

>However, some of the proposals we have been discussing, e.g., adding chemical
>information to identify molecules etc., will be deferred to CIF3,

'  I am of the irritating opinion that identification of molecules in CIF is too important to await CIF3.
  
' As my final fling as chairman of the IUCr Committee on Electronic Publishing (and in order to avoid having my dislocated and fractured shoulder jostled in the poster sessions) in Florence I sat through a good number of the open and closed commission meetings on matters concerned with publication, electronic or otherwise.  Of the utmost relevance concerning the addition of chemical information to CIF were the public and private utterances of various representatives of the CCDC.  As internally (to the database) they have become more and more CIF-oriented over the years, they had reached the point of needing to define their local (private) CIF dictionnary for encoding chemical and molecular information.  I understood that much of the ground work had been done, and the choice of data names and definitions was imminent (in August 2005).  If they have gone ahead with this work, their dictionnary will become the de-facto standard.'

IDB Comment:

Howard later agreed that he might have exaggerated the urgency for this move by in any case I will see whether it might be possible to come up with a quick way to identify molecules and map them onto the crystallographic structure.
 
A2. REPORTING CONSTRAINTS AND RESTRAINTS.
----------------------------------------

This discussion is prompted by the proposal to extend the enumeration list of _atom_site_refinement_flag_adp presented below (B8), but it raises some questions that are best dealt with separately.  

My attempt to define the difference between a constraint and a restraint provoked a lively and unrestrained discussion.  Although some of these suggestions have been made before, they need to be resolved.

>   8.  _ATOM_SITE_REFINMENT_FLAG_ADP 
> [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.

Howard Flack writes: 
'There is a confusion in your comment.  A 'constrained parameter' may very well be refined. An atom on a special position such as x, x, x is having the atomic coordinates x, y and z refined by least-squares but constrained such that y = x and z = x. y and z are variable during the least squares and take new values each cycle. From your sentence one could believe that you think for the special position x, x, x that the y and z coordinates take fixed values during a least-squares cycle and are reset to the new value of x at the end of the cycle.'

>A 'restraint' is a target value for some structure dependent
> variable (not one that is being refined)

'  I'm sure that is not quite right either.  For shift-limiting restraints and polar-axis restraints there is no target value. Likewise for similar-molecule restraints.'

IDB Comment:
As HF's comment shows, my definitions of constraint and restraint given above are clearly inadequate.  What about:

# 'A potentially refinable parameter is said to be constrained
# if, after a given round of least squares refinement the
# parameter is set to a predetermined fixed value or to a value
# calculated from other refined parameters or some combination of
# these. 
# Crystallographic symmetry requires some parameters to be
# constrained, but because such constraints are required by the
# space group setting adopted, it is not customary to include
# them explicitly in the list of constrained parameters.'

# 'A parameter that can be calculated from one or more of the
# refined parameters is said to be restrained if it is assigned a
# target value and standard uncertainty.  It is customary to treat 
# restraints as observations along with the structure factors.'

This does not deal with the case where only a fraction of the indicated shift is applied.  Perhaps this needs a different name.

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

STATUS: open for discussion.
  
George Sheldrick raises a more general matter that stimulated a number of suggestions.

'Since restraints and constraints have come up again I cannot resist commenting. The main reason why it is not possible to reproduce a crystal structure refinement from the data in CIF file is that most of the information about the restraints and constraints that were applied in the refinement 
has been lost or degraded. It is no secret that the majority of small 
molecule structures are refined with a program called SHELX. The last 
time a change was made to the definitions of the restraints and 
constraints used by that program was 1993. In fact many of them date 
back to the 1976 version. Surely we have had enough time to find a way 
of incorporating this information properly into a CIF file? Otherwise I 
may feel obliged in the next version of SHELX (if there is one) to embed 
the .res file - which contains all this information in a concise and 
unambiguous form - into the CIF file, as many users have requested.'

Ton Spek writes:
'Essentially, the inclusion of the shelxl.res as 'detail section' in the
CIF has been suggested at several occasions and settings, including the
Acta editorial board.
Unfortunately, no follow-up was given to this up-to-now.
The only thing that would help is an update of the SHELXL software in
this respect.'
	
Syd Hall writes:
'I have just seen the COMCIFS input by George. Its not a
new comment; for the last decade at least he has claimed that it would be much simpler for everyone to archive a shelx file with all his encrypted codes
than worry about this generalized nonsense! :)  In other eras Bill Busing,
Jim Stewart and Carroll Johnson could make the same argument
for their then dominant formats... I guess they did, but not
much of that archived data is useful today.

'Anyway I am not buying into this exchange... It opposes
all of the seamless data exchange and long-term archiving principles.
It is an appealing brainless option for shelx users, most of
whom do not understand constraint relationships anyway, to dump
a shelx file into a text item but it's certain to prove a disaster
for future data mining in CIF or XML files.  Are the objectives of long-term archiving that hard to understand?'

Herbert Bernstein writes:
   'As an outside observer of the core discussions, may I suggest that
that you may be considering a false trichotomy:
   1.  Deferring detailed restraint and constraint information until CIF3; or
   2.  Incorporating the restraint and constraint information now; or
   3.  Sidestepping by incorporating the .res information from
SHELX or similar parsable-but-not-yet-CIF-parsed information
from other refinement programs.
Why not do all three?
   'Certainly, the features of CIF3, allowing methods will facilitate the
presentation of complex constraints, and, when CIF3 is available, this would
be an area in which to use methods effectively.  However, there is no
reason not to include as much as can be included now under fully parsed
CIF tokens, _and_ to carry the "raw" constraint information in, say, a
"...details" tags immediately.
   'We are facing a similar problem in the imgCIF dictionary.  Images come
from the vendors with wonderfully detailed headers containing essential
information.  We have tags to carry much of the same information, but
things evolve and things are missed.  So we have proposed to add a new
tag to our dictionary (in this case _diffrn_data_frame.details, described
as "A description of special aspects of each frame of data.
     This is an appropriate location in which to record
     information from vendor headers as presented in those
     headers, but it should never be used as a substitute
     for providing the fully parsed information within
     the appropriate imgCIF/CBF categories.")
   'This is being done in response from a vendor to carry the "raw"
header information in a comment.  Giving it a tag preserves the
information in a form that allows it to be examined both by
users and by software and which encourages the use of existing
tags for the detailed information and encourages the creation of
the necessary new tags to carry what has not been handled yet.
   'While this may lead to the same information being presented in
more than one place, that is just what we already do with various
"...details" tags, and having information in multiple places in
a CIF is a lot better than having the information lost.
   'Therefore, I suggest that you:
   3a.  Immediately add a "...details" tag to carry detailed
refinement program settings and values in as close to "raw" form
as possible and in particular to carry the .res information
from SHELX; and
   2a.  As time permits that you add and update CIF tags for
constraints and restraints to whatever extent you can achieve
agreement, but without removing information from the "...details"
tag; and
   1a.  When we have CIF3, that you use its powerful features to
carry even more of the constraint/restrain information in detailed
parsable and executable form.
Perhaps you might consider using, say, _atom_sites_refinement_details
for item 3a, as
     "A description of special aspects of the refinement.
     This is an appropriate location in which to record
     information from refinement programs as presented in
     .res files, etc, but it should never be used as a substitute
     for providing the fully parsed information within
     the appropriate CIF categories."
Alternatively, you could use _atom_sites_special_details,
which already exists, but which does not seem to have a clear
purpose in life.  This would give it such a purpose.'

IDB comment:
SH's comment about the long term viability of the archive is central to the philosophy of CIF and should be taken seriously.  Including the .res file in a text field is at best a short term fix and at worst an excuse for not giving the information in a CIF-readable form that is precisely defined in the CIF dictionary. 

However having said that, I should point out that there is currently nothing to stop anyone from including all or part of a .res (or any other) file in  atom_site_constraints, _atom_site_restraints, _atom_sites_special_details or _refine_special_details.  This would not violate any CIF rules however much this may be deprecated by CIF purists, but to my knowledge no one has ever done this.  Of course a CIF compliant application would not necessarily be able to use this information and nor could a CIF user find how to decode the .res information by referring to the CIF dictionary.  

I have however accepted an offer from Ilia Guzei of Wisconsin to prepare a full CIF description of restraints and constraints and he and I are already well on the way to producing what you have all been waiting for.  The restraints dictionary looks as if it will be large but I will circulate it once we have it worked out.

STATUS: Awaiting Ilia's proposal.

#########################################################
#
# B. CHANGES PROPOSED FOR SPECIFIC ITEMS IN THE CORECIF DICTIONARY
#
#####################################################################
#
# Items in Discussion Paper #8 recommended for dropping have now been dropped.
# Items in Discussion Paper #8 recommended for approval have now been added to
# the list of approved items.  This list will eventually be circulated again
# for final approval.
#
########################################
#
#  SUMMARY OF ITEMS REQUIRING FURTHER DISCUSSION OR APPROVAL
#
########################################
#
#  5. _GEOM_BOND_MULTIPLICITY                   Recommend acceptance
#
#  6. _EXPTL_ABSORPT_CORRECTION_T_max and T_min Recommend acceptance
#
#  7. REFINE_ELECTRON_DENSITY                   Recommend dropping
#
#  8. _ATOM_SITE_REFINMENT_FLAG_ADP             Open for discussion
#
#  9. _ATOM_SITES_SOLUTION_*                    Recommend acceptance
#
#  10._CHEMICAL_ENANTIOEXCESS_BULK_*            Recommend acceptance
#
#  11._PUBL_SECTION_KEYWORDS				Recommend acceptance
#
#  12. DIMENSIONLESS UNITS                      Recommend dropping
#
##########################################
#
#  B5. _GEOM_BOND_MULTIPLICITY
#
##########################################
#
# COMMENT: In high symmetry structures when many bonds are related by symmetry
# it may not be 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 give a multiplicity 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.  In cases where the 
        full list of bonds is given, one of the series of equivalent bonds may
        be assigned the appropriate multiplicity while the others are assigned
        a value of 0.
;
#
# Brian McMahon and Peter Strickland write:
# Acta Cryst. journal policy is to encourage the listing of all bonds in the
# CIF; and current journal policy is not to print bond distances unless they
# are unusual (in which case it's probably unlikely that an n-fold
# symmetry-generated bond would be printed anyway). Overall, we're neutral
# about including such a new item. It would be helpful to give an example (in
# the GEOM_BOND category block) that illustrates such a case, and perhaps
# demonstrate that it can co-exist with individual specific bond listings: if
# we decide to go ahead with this item I'll see whether we can find useful
# examples in the literature.
#
# IDB replies:
# I give a couple of examples below.  Note that in the second case it would be
# wrong to use . or ? instead of 0.  The zero is sufficient to ensure that the
# second list could be automatically reduced to the first list.  There is no
# default value for this item. 
#
loop_
_example_detail
_example
'An example showing a listing of only the symmetry unique bonds'
;
loop_
_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_geom_bond_distance
_geom_bond_multiplicity
Ca1   F1   2.495(9)    1
Ca1   F2   2.291(10)   2
Ca1   F2   2.391(11)   2
Ca1   F3   2.214(11)   2
Cr1   F1   1.940(11)   2
Cr1   F2   1.918(9)    2
Cr1   F3   1.848(10)   2
;
'An example where the multiplicity is given with a full bond list'
;loop_
_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_geom_bond_site_symmetry_2
_geom_bond_distance
_geom_bond_multiplicity
Ca1   F1   1_555  2.495(9)    1
Ca1   F2   1_555  2.291(10)   2
Ca1   F2   2_555  2.291(10)   0
Ca1   F2   3_565  2.391(11)   2
Ca1   F2   4_555  2.391(11)   0
Ca1   F3   2_545  2.214(11)   2
Ca1   F3   5_555  2.214(11)   0
Cr1   F1   1_555  1.940(11)   2
Cr1   F1   2_555  1.940(11)   0
Cr1   F2   1_555  1.918(9)    2
Cr1   F2   2_555  1.918(9)    0
Cr1   F3   1_555  1.848(10)   2
Cr1   F3   2_555  1.848(10)   0
;
#
# STATUS: Recommended for approval
#
###########################################
#
# B6. 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 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.
#
# 5. how should these be interpreted in the case of multiple wavelengths
# where the transmission factors depend on wavelength?
#
# BM & PS write:
# It may be helpful to state in a little more detail what current Acta
# practice is. The transmission factors are calculated by PLATON and
# compared against _exptl_absorpt_correction_T_max and *_min. If they
# differ, we store the calculated values as
# _iucr_exptl_absorpt_correction_T_min and *_min (not very
# expressive, but at least clearly distinguishable tags). In other
# words, our practice implies that the existing items are handled as
# in your item (1), and calculated transmission factors (2) are also
# stored if they are identified as different. It would therefore help
# us if the definition (1) were adopted and a new "official" item
# introduced for (2). This distinction has however been made only
# comparatively recently, so it is possible that older CIFs have used
# the data items in the sense of (2).
#
# RECOMMENDATIONS
#
# That we reword the definition of _exptl_absorpt_correction_T_max and T_min
#
_definition
     The maximum and minimum transmission factors applied to the diffraction
     pattern measured in this experiment.  
     These factors are also referred to as the
     absorption correction A or 1/A*.
     As this value is the one that is applied to the measured intensities, 
     it includes the correction for
     absorption by the specimen mount and diffractometer as well as by the
     specimen itself.
#
# and that we introduce new items:
#
data_exptl_transmission_factor_max
    _name               '_exptl_transmission_factor_max
    _category            exptl        
    _type                numb        
    _type_conditions     su        
    _enumeration_range   0.0:1.0
    _definition
;              The calculated maximum value of the transmission factor for the                 specimen.  
               The presence of this item does not imply that an absorption
               correction has been made, and its value does not include the
               effects of absorption in the specimen mount.
;
data_exptl_transmission_factor_min
    _name               '_exptl_transmission_factor_min
    _category            exptl        
    _type                numb        
    _type_conditions     su        
    _enumeration_range   0.0:1.0
    _definition
;              The calculated minimum value of the transmission factor for the
               specimen.
               The presence of this item does not imply that an absorption
               correction has been made, and its value does not include the
               effects of absorption in the specimen mount.
;
#
# The wavelength is irrelevant since only the smallest and largest values
# of the transmission factors are recorded and these are determined at
# whatever wavelength gives rise to these extremes.
#
#################################
#
# STATUS: Recommended for adoption
#
#################################
#
# Relevant to this discussion are comments received from Ross Angel who is
# is writing a program for reporting high-pressure results as CIF.
#
# He 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.
#
# [IDB: This information can be included in a special_details field, but a
# flag is unnecessary and perhaps undesirable as it could be misused by
# people as a way of getting their CIF through checkcif without raising a
# warning.  It is the task of the user, reviewer or editor to decide whether
# the lack of completeness is an issue]
#
# 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.
#
# [IDB: The definitions above address this concern.]
#
# 3) A way to document the corrections for the absorption and shadowing by the
# pressure cell
#
# [IDB: This could be included in _exptl_absorption_process_details 
# or _exptl_special_details]
#
# 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 comment:
# RA 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.
#
# Note that this convention is different from the one adopted by RA, but he
# describes his convention so that conversion is possible, at least for a
# conventional diffractometer.
#
######################################################################

##########################################
#
#  B7. 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 being supplied to the contrary, 
# one would assume that these peaks are those found in the final electron
# density map, but the examples given below suggest that it might intended for
# 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.  
#
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.
;

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.
;
#
# As there was no discussion of this item following the Discussion Paper #8,
# and because there are a number of unanswered questions about the definition
# and usefulness of this category, I would propose that we drop this item;
#
# STATUS: Recommend dropping
#
########################################
#
#   B8.  _ATOM_SITE_REFINMENT_FLAG_ADP
#
########################################
#
# Curt Haltiwanger suggests that we need to extend the enumeration list for
# this item.  
#
# IDB COMMENT:
# Curt's suggestions (which I have not included here do not provide a rigorous
# definition of how the
# constraints were applied and only make the CIF more complicated. 
# 
# STATUS: I recommend dropping this item and waiting until Ilia and I
# complete our proposal for the description of restraints and constraints.
#

#######################################
#
#  B9.  _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: Recommend acceptance (can someone provide a reference?)
#

#######################################
#
# B10. _CHEMICAL_ENANTIOEXCESS_BULK_*
#
#######################################
#
# Howard Flack (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
    _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
;
                                 Other
;                                     ensntioexcess determined by 
                                      a technique not described in the         
                                      enumeration list
;
    _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_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
;
                                 Other
;                                     ensntioexcess determined by 
                                      a technique not described in the         
                                      enumeration list
;
    _definition
;              The experimental technique used to determine the
               enantioexcess of the crystal.
;
# HDF writes:
#----------
#  Please note that the data items in this section have the same limitation as
#  _chemical_absolute_configuration.  They refer to a compound i.e. a 
# collection of molecules, and it is not possible at present to identify
# molecules in CIF.
#
# IDB: I have added 'other' to the enumeration lists to take account of
# possible future developments.  I will see if some quick fix to defining a
# molecule is possible.
#
# STATUS: Recommend acceptance.
#

#################################
#
#  11. _PUBL_SECTION_KEYWORDS
#
#################################
#
# Doug Boulay (05-06-25) writes: 
#------------------------
# After reading David's report,
# I notice 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]
#
# Brian McMahon and Peter Strickland write
#
# We agree that at present such an item would be useful but
# should not be constrained by an enumeration list. The broader
# area of keywords specifying scientific topics is one we want
# to come back to at a later date.
#
data_publ_section_keywords
    _name               '_publ_section_keywords'
    _category           publ         
    _type               char         
    _list               yes
    _example                       ?
    _definition         'Keywords associated with the manuscript'
#
# STATUS: Recommended for adoption
#

########################
#
# B12. 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 ComitÃ© 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: 'uno' could easily be added to the list of units but see the comment
# below.]
#
# BM & PS write:
#---------------
# A report of the IUPAP General Assembly 2005
# (http://www.iupap.org/commissions/c2/reports/ga-05.html)
# suggests that SI adoption is at least some way off:
#
#   The Uno: The introduction of a name, 'uno', for the unit one in SI was
#   proposed by the CCU of the BIPM (see RenΘ Dybkaer, Metrologi a, 41
#   (2004) p.69-73) . It was decided that because of the potential
#   inconsistencies that might result from the introduction of such a unit,
#   the commission could not support the introduction of this new unit. The
#   matter has been dropped for the time being by the CCU.
#
# We are somewhat concerned about the proposal in any case. Proportionality
# is indeed dimensionless, but it seems that one is throwing away information
# if one does not record that proportionality is by volume, mass, etc.
#
# This matter should be tracked by the Nomenclature Commission, but we
# recommend that no action be taken before any formal adoption of the uno
# into the SI system - the topic can then be raised again for discussion if
# desired.
#
#
# STATUS: Recommend this item be dropped for the reasons given by BM & PS.
#
################################