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Comments on CIF core changes for 2.3

  • To: Multiple recipients of list <[email protected]>
  • Subject: Comments on CIF core changes for 2.3
  • From: "Haltiwanger, Curt" <[email protected]>
  • Date: Sat, 12 Jul 2003 18:28:35 +0100 (BST)
I have the following comments and questions based on the
cifCoreDic-2.3approved.txt attached to Brian's e-mail of July 10

data_atom_site_refinement_flags_adp
    _name                      '_atom_site_refinement_flags_adp'
    _category                    atom_site
    _type                        char
    _list                        yes
    _list_reference            '_atom_site_label'
    loop_ _enumeration
          _enumeration_detail
          .  'no constraints on atomic displacement parameters'
          T   'special-position constraints on atomic displacement
parameters' 
          U  'Uiso or Uij restraint (rigid bond)'
          TU 'Both constraints applied'
    _definition
;              A code which indicates the refinement restraints or
constraints
               applied to the atomic displacement parameters of this site.
;
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   These would also be a
candidate for enumeration.   I have no knowledge of the restraints and
constraints used in other programs.

So
          S   'special-position constraints on atomic displacement
parameters' 
          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 )'         


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

data_atom_site_refinement_flags_occupancy
    _name                      '_atom_site_refinement_flags_occupancy'
    _category                    atom_site
    _type                        char
    _list                        yes
    _list_reference            '_atom_site_label'
    loop_ _enumeration
          _enumeration_detail   . 'no constraints on site occupancy
parameters'
                                P 'site occupancy constraint'
    _definition
;              A code which indicates that refinement restraints or
               constraints were applied to the occupancy of this site.
;

What is partial occupancy constraint?  
The most common restraint to occupancy is that the occupancies two partial
occupancy sites sum to a constant (usually  1. but 0.5 etc for special
position sites)  Also if the disorder is over three or more positions the
sum of the occupancies can restrained to be a constant.

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

data_diffrn_reflns_measured_fraction_resolution_full
     _name                '_diffrn_reflns_measured_fraction_resolution_full'
     _category                  diffrn_reflns         
     _list                      yes
     _type                      numb
     _enumeration_range         0:1.0
     _related_item             '_diffrn_measured_fraction_theta_full'    
     _related_function          alternate
     _definition
;         Fraction of unique (symmetry-independent) reflections measured
          out to the resolution given in _diffrn_reflns_resolution_full.
          This number should be very close to 1.0, since it represents the
          fraction of reflections measured in the part of the diffraction
          pattern that is essentially complete.
;
# COMMENT: Replacement for _diffrn_measured_fraction_theta_full, moved to a
# more appropriate category and defined in terms of resolution rather than
# angle which depends on the radiation used.
# 2003-06-26 _related_function 'replace' changed to 'alternate'
# STATUS: Preliminary approval 2002-11-11


There is the potential for confusion here.  
We currently have 
_diffrn_measured_fraction_theta_full
_diffrn_measured_fraction_theta_max
_diffrn_reflns_theta_full
_diffrn_reflns_theta_max
and we are adding
_diffrn_reflns_measured_fraction_resolution_full
_diffrn_reflns_measured_fraction_resolution_max
_diffrn_reflns_resolution_full
_diffrn_reflns_resolution_max

In the experiment, I would think that
_diffrn_reflns_measured_fraction_resolution_full (or _max)
will be the same as the _diffrn_measured_fraction_theta_full (or _max).   I
can see the value of talking in terms of resolution rather than theta,
(although I am more comfortable with angles) but why have two data names
that describe the same number. Why not define terms
_diffrn_reflns_measured_fraction_full and
_diffrn_reflns_measured_fraction_max 
leaving out all reference to whether it is based on resolution or theta

In addition the numbers currently being reported by a popular refinement
program are based on what that refinement program is receiving as input, not
what the data reduction program (integration program) had as input or
output. Do we need or want entries similar to what currently exists in the
dictionary for this situation. 
For example reflns_limit_ and diffrn_reflns_limit_ where the two values do
not need to be the same as the first refers to the values used for
refinement and the second to values in the data collection. 
Which are the more relevant numbers, the numbers related to refinement, or
measurement, or both?
 
 
######################################################################

data_diffrn_standards_decay_%_lt
    _name                      '_diffrn_standards_decay_%_lt'
    _category                   diffrn_standards
    _type                       numb
    _related_item               '_diffrn_standards_decay_%'
    _related_function           alternate
    _enumeration_range          :100
    _definition
;              An upper limit on the percentage decrease in the mean
               intensity of the set of standard reflections measured at the
               start of the measurement of the diffraction pattern and at
the
               end. This value is used when the decay is too small to be
               detected.
;
# COMMENT: Many experiments show no detectable decay and there is no
provision
# for this at the moment other than to enter 0.0.
# STATUS: Preliminary approval 2002-11-11

I like the concept, but I wonder about its usage to create tables.  I have
never written
such programs, but seems complicated to me to have a table entry for crystal
decay that looks at two different cif items to decide which one to use.  
 
I would guess that this item is being introduced because crystal decay is
almost certainly never 0.0%.  Wouldn't it be simpler to change the
definition of  '_diffrn_standards_decay_%' to reflect that decay corrections
are approximate, not exact numbers.

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


data__diffrn_reflns_measured_fraction_resolution_max
    _name                '_diffrn_reflns_measured_fraction_resolution_max'

There is a double __ here.

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


# 
# THE PREVIOUS ITEM REPLACES _symmetry_cell_setting.  The definition of the
old
# item should be modified to make it clear that the old name is discontinued
# (the name is crystallographically incorrect and therefore misleading).
The
# following items should be added to the dictionary entry for
# _symmetry_cell_setting:
#
#    _related_item        '_space_group_crystal_system'
#    _related_function    replace
#
# Incidentally I have removed the _related_item and _related_function from
the
# definition of _space_group_crystal_system because they are incorrect.  It
is
# the _related_item that should 'replace' the item being defined, not the
other
# way around.
#
So what happens to _space_group_crystal_system??   Should there be a
replaced or obsolete.


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



data_space_group_symop_operation_xyz
    _name              '_space_group_symop_operation_xyz'
    _category          space_group_symop
    _list              both
    _list_mandatory    no
    _list_reference    '_space_group_symop_id'
     loop_
    _example
    _example_detail
              'x,1/2-y,1/2+z'  'c glide reflection through the plane
(x,1/4,z)'
    _definition
;               A parsable string giving one of the symmetry operations of
the
                space group in algebraic form.  If W is a matrix
representation
                of the rotational part of the symmetry operation defined by
the
                positions and signs of x, y and z, and w is a column of
                translations defined by the fractions, an equivalent
position
                X' is generated from a given position X by the equation:

                          X' = WX + w

                (Note: X is used to represent bold_italics_x in
International
                Tables for Crystallography Vol. A, Section 5)

                When a list of symmetry operations is given, it is assumed
                that the list contains all the operations of the space
                group (including the identity operation) as given by the
                representatives of the general position in International
                Tables for Crystallography Vol. A.
;
    _type              char
 
    _enumeration_default   'x,y,z'

# STATUS: Preliminary approval 2003-03-11

Doesn't c-glide define reflection and if so isn't reflection redundant?  
I don't see how the example detail helps the definition.  I would like to
see a fuller example but I do not know how to set it up to give something
that looks like this.  

Thus for the symmetry operators for 
P212121 should be
x,y,z
-x,1/2+y,1/2-z
1/2-x,-y,1/2+z
1/2+x,1/2-y,-z

and for C2/m (setting  ???? ) 
x,y,z
x,1/2-y,z

or should it be

and for C2/m (setting  ???? ) 
x,y,z
-x,-y,-z
x,1/2-y,z
-x,1/2+y,-z1/2+x,1/2+y,z
1/2-x,1/2-y,-z
1/2+x,-y,1/2+z
1/2-x,y,1/2-z

I must admit that until I read (or misread) Howard's comments I would have
made C2/m look like the simpler example.
The suggested extended examples could help resolve ambiguities.  Perhaps the
extended example could also include a non standard setting.   

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

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