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RE: core CIF discussion #6
- To: Distribution list of the IUCr COMCIFS Core Dictionary Maintenance Group <coredmg@iucr.org>
- Subject: RE: core CIF discussion #6
- From: "Haltiwanger, Curt" <CHaltiwanger@bruker-axs.com>
- Date: Thu, 3 Jun 2004 10:25:05 -0500
Comments on CIF discussion #6
David, thanks for the expansion of the CIF statements. A good feeling for a
CIF is found by looking at them all.
How's this?
The CIF should be a useful easy to read file that allows a crystallographer
to archive
details of the experiment and to evaluate the quality of a reported result.
In addition to archiving data, it should facilitate data exchange between
software within a laboratory and between different laboratories. The CIF
should
facilitate electronic input to the publication process and allow easy data
exchange
between authors and journals and computerized databases. The cif must also
allow
crystallographers and other scientists access to the data in a useful
interpretable
way for statistical studies.
Using only a few simple syntax rules the CIF is based on a data structure
that is
completely self-defined with order independent self-defined data items.
RCH comments
Item #6
I am quite happy to see item 6 change into an editorial change only and I
approve of the change of the enumerator U to be a restraint or constraint
not related to symmetry......
This eliminates my need to decide if a U that is 1.2 times the Ueq of the
attached atom is a restraint or a constraint. By the way, I have it on good
authority (David Watkin and George Sheldrick) that this is a constraint as
it is held constant during a given least-squares refinement cycle and
shifted between cycles.
But it also means we are not capturing all of what is needed to pass data
from on piece of software to another.
For that reason I restate my request for a _refine_input_details which would
be in addition to the
_refine _special_details which would remain a place to put "Description of
special aspects of the refinement process. "
As I envision it would be something like the following, but I don't like the
reference to specific programs in the example.
data_refine_input_details
_name '_refine_input_details'
_category refine
_type char
_list no
_example 'SHEXL.ins file or the Crystals constraint
and restraint list as input by the user'
_definition
; A copy of the input file or the constraint and restraint
information used for
the refinement.
;
With crystallographers and noncrystallographers doing 100s of structures a
year, I can not imagine many cases where a written description of the
special details of the refinement is going to be included in the cif. It
would be wonderful, but it is not likely to happen. If it is required, the
scientists will send there cifs to somewhere that does not have the
requirement. If there is a written description, it should not get combined
with a least-squares input file.
Item #7
I agree drop
Item #8
I agree with the change to count. I'd add to the example,
... bonds around Ni1, where Ni1 is part of an NiO6 moiety sitting at a
position of 4/m symmetry.
Should the definition include the idea of symmetry in the definition.
Perhaps "....appears (as the result of symmetry) in the environment of the
atoms labeled ....'
Item #9
Drop - hope there is no huge outcry
Item #10
I think this is a good idea, but I am having trouble imagining its use.
Since it is associated with sites, plural, I assume that it refers to all
hydrogen sites. Is that correct? Is that a usual occurrence? In small
molecule organics, the hydrogen atoms are often taken from a difference map
and refined when attached to heteroatoms, calculated when on carbon atoms,
and occasionally not determined for the water molecules. The same would be
true of organomatallics. Frankly I don't think I have ever used
_atomic_sites_solution in any cif I have written or worked with. How many
examples are there? If only a few then add 'notdet' and not worry about
mixed situations, though those are probably the most common in reality.
Item #11
This is a nice addition. When will all least-squares programs be able to do
this?
Given the, albeit slim, possibility of confusion between d for determined
from diffraction and dummy, should we add
det 'Determined directly from diffraction measurements' (or should it be
dif for "Diffraction data" )
d 'abbreviation for determined or diffraction'
m 'abbreviation for duMmy site with Meaningless coordinates
AND
encourage the use of the three or four letter codes.
On my printout and in the version below the lines are wrapping "an1 dum"
to separate lines.
This confuses the example and care should be taken to make sure that does
not happen routinely.
I assume that an1 and an2 refer to annulus1 and annulus2 Perhaps saying
something like
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 .
;
In the list of shapes, why not include an ellipsoid. While this may not be
a choice in Crystals it seems like a logical shape to have in the list.
-----Original Message-----
From: David Brown [mailto:idbrown@mcmaster.ca]
Sent: Monday, April 26, 2004 11:00 AM
To: coredmg@iucr.org
Subject: core CIF discussion #6
Core CIF Discussion #6
Dear Colleagues,
I enclose below Discussion Paper #6 in the current round of changes
proposed for the core CIF dictionary. This round contains five items
from the
Discussion paper #5 with recommendations for the approval of some items and
dropping of others. There is also a new item proposed by David Watkin for
recording information about refinements using distributed scattering density
such as a rotating ring of charge.
This email prints out on around 17 pages. Can you please check through
the items presented and send your comments to the core CIF discussion
group at
coredmg@iucr.org? I will start working on the next round after June 30
which
is therefore the deadline for receiving comments. If you need more time let
me know. The deadline is flexible.
Best wishes
David Brown
-------------------------
General comment by Curt Haltiwanger
-----------------------------------
My perspective on cifs in general is -
The cif should be a useful tool that allows a crystallographer to store
details of the experiment and to evaluate the quality of a reported result.
The cif must also allow crystallographers and other scientists access to the
data in a useful interpretable way for statistical studies.
My responses are driven by this perspective and my experience in single
crystal x-ray diffraction. I'd be interested in hearing the official mission
statement. I wonder how close I am. ???
Response by IDB.
----------------
I am not sure that there is an official mission statement for CIF but Curt's
summary is as good as any. The nearest official mission statements I
can find
are found in the original paper by Hall, Allen and Brown Acta Cryst. (1991)
A47, 655-685:
'In addition to archiving data, the use of a universal file would facilitate
data exchange between software within a laboratory; between different
laboratories; between authors and journals, providing electronic input
to the
publication process; and between researchers or journals and computerized
databases.'
and in Syd Hall's account of the STAR file structure (J. Chem. Inf.
Comp. Sci.
(1991) 31, 326-333) the properties of a STAR file are given as:
'The data structure is completely self-defined
The data items are completely self-defined
The syntax rules are few and simple
The data may be in any type and in any order
The file is easy to read visually or by machine'
Perhaps between the three statements one can distill the flavour of CIF.
####################
#
# Items included below Recommendation
# -----------------------------------------------------------------
#
# Item 6 Atom_site_refinement_flag_ Editorial changes only
#
# Item 7 diffrn_refln_status Drop
#
# Item 8 _geom_bond_count Approve
#
# Item 9 _refine_scattering_density Drop
#
# Item 10 _atomic_sites_solution_hydrogen Approve
#
# NEW ITEM
#
# Item 11 Distributed scattering density Discussion
#
##########################################
#
# Item 6.
#
##########################################
#
# _atom_site_refinement_flag_adp
#
# Carried over from discussion #4
#
# There has been extensive discussion of this item which is designed to
# indicate the constraints or restraints applied to the ADP. On one
hand, it
# has been suggested that we should define a sufficient number of flags that
# someone could repeat the refinement. On the other hand, there are so many
# different ways of applying restraints that enumerating all the
possibilities
# becomes impossible. All we can reasonably do is place a flag to warn the
# reader that at least some parameters were not freely refined, leaving
# further details to be given in the existing items
_atom_site_constraint and
# _atom_site_restraint for individual atoms, or _refine_special_details
for a
# more general description.
#
# Curt Haltiwanger (04-02-27) has written at length on this matter, and I
# extract part of his comment (his full comment is available as part of our
# discussion on the IUCr web site).
#
# Curt writes:
# ------------
# 'However I am having trouble figuring out whether the Uiso on a hydrogen
# atom that is set to 1.2 time the Ueq of the atom it is attached to
would be
# constraint or a restraint or something else. This is common situation in
# many or most structures with C-H's refined with SHELXL. As I see it this
# treatment of hydrogen atoms does not fit either of the definitions for
# constraints and restraints. I think it is important that we provide data
# items that allow users to report what they actually do.....
#
# I think it would be quite useful to have an official cif entry similar to
# _refinement_special_details, that would contain a copy of the refinement
# input file. Would _refinement_input_file be a possibility? I realize
that
# this file would be of no use to anyone who did not have access to that
# particular program or to a users manual for the program. I think it
is much
# more significant that the scientist who did have access to the program or
# manuals would have access to the information that it is almost impossible
# for the cif to capture. If someone did not have immediate access, they
# would still have the option of getting a version of the program. At least
# the details would be present and the devil is in the details.
#
# 'So I don't think that we have exactly the right definition yet. And I
# think that we need a way of including input files in the cif.'
#
# IDB Response:
# -------------
# The person preparing a CIF has the option to put anything they like in the
# various special_details and similar text fields, including the input
file to
# the program they used, though a verbal description of the procedure
would be
# more informative since it would be intelligible to people who did not have
# access to the program. I list below some of the items that are already in
# the approved core dictionary, and these would seem to provide sufficient
# opportunities for recording the restraints and constraints applied during
# refinement. In the interests of keeping things simple, I recommend
that we
# make no change to these items (except for the editorial changes noted).
#
# The following seven items are taken from the latest approved coreCIF
# dictionary (version 2.3). They provide plenty of space to describe a
# variety of different kinds of restraints. Some possible editorial changes
# are suggested.
#
data_atom_site_refinement_flags_adp
_name '_atom_site_refinement_flags_adp'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
_related_item '_atom_site_refinement_flags'
_related_function alternate
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)'
#
# A better _enumeration_detail for the above line might be:
# ; A restraint or constraint not related to symmetry applied to the atomic
# displacement parameters.
# ;
#
TU 'Both constraints applied'
_definition
; A code which indicates the refinement restraints or
constraints
applied to the atomic displacement parameters of this site.
;
#
# The definition might better read 'A code that indicates that refinement
# restraints or constraints were applied...'
#
data_atom_site_refinement_flags_occupancy
_name '_atom_site_refinement_flags_occupancy'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
_related_item '_atom_site_refinement_flags'
_related_function alternate
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.
;
data_atom_site_refinement_flags_posn
_name '_atom_site_refinement_flags_posn'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
_related_item '_atom_site_refinement_flags'
_related_function alternate
loop_ _enumeration
_enumeration_detail
. 'no constraints on positional coordinates'
D 'distance or angle restraint on positional
coordinates'
G 'rigid group refinement of positional coordinates'
R 'riding-atom site attached to non-riding atom'
S 'special position constraint on positional
coordinates'
DG 'combination of the above constraints'
DR 'combination of the above constraints'
DS 'combination of the above constraints'
GR 'combination of the above constraints'
GS 'combination of the above constraints'
RS 'combination of the above constraints'
DGR 'combination of the above constraints'
DGS 'combination of the above constraints'
DRS 'combination of the above constraints'
GRS 'combination of the above constraints'
DGRS 'combination of the above constraints'
_definition
; A code which indicates the refinement restraints or
constraints
applied to the positional coordinates of this site.
;
data_atom_site_calc_attached_atom
_name '_atom_site_calc_attached_atom'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
#
# This item should be shown as being a child of _atom_site_label
#
_enumeration_default '.'
_definition
; The _atom_site_label of the atom site to which the 'geometry-
calculated' atom site is attached.
;
data_atom_site_calc_flag
_name '_atom_site_calc_flag'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
loop_ _enumeration
_enumeration_detail d 'determined from diffraction measurements'
calc 'calculated from molecular geometry'
c 'abbreviation for "calc"'
dum 'dummy site with meaningless coordinates'
_enumeration_default d
_definition
; A standard code to signal if the site coordinates have been
determined from the intensities or calculated from the
geometry
of surrounding sites, or have been assigned dummy
coordinates.
The abbreviation 'c' may be used in place of 'calc'.
;
data_atom_site_constraints
_name '_atom_site_constraints'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
_enumeration_default '.'
_example 'pop=1.0-pop(Zn3)'
_definition
; A description of the constraints applied to parameters at
this
site during refinement. See also _atom_site_refinement_flags
and _refine_ls_number_constraints.
;
data_atom_site_restraints
_name '_atom_site_restraints'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
_example 'restrained to planar ring'
_definition
; A description of restraints applied to specific parameters at
this site during refinement. See also
_atom_site_refinement_flags and _refine_ls_number_restraints.
;
#
# The above two items should reference each other in the definition
#
# STATUS: Recommend only editorial changes
#
#######################################
#
# Item 7
#
#######################################
#
# _diffrn_refln_status
#
# COMMENT: The purpose of this proposed item is to allow reflections
that are
# believed to be systematically absent during measurement to be flagged, but
# the question was raised, 'Where do we identify the assumed space group and
# in any cases does this flag make any sense?'
#
# Note that there is already an item _refln_refinement_status with
values of:
# incl(uded in refinement), excl(uded from refinement) and extn
(extinguished,
# i.e. systematically absent. This flag is based on the space group used in
# the refinement and reported in the CIF.
#
# There is a persuasive lack of enthusiasm for this item and I propose
that we
# drop it. For this reason I have commented out the definition below. I
# have, however, included an extract from Curt's comments at the end of this
# section where he raises another question.
#
#data_diffrn_refln_status
#_name '_diffrn_refln_status'
#_category diffrn_refln
#_type char
#_list yes
#_list_reference '_diffrn_refln_index_'
#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 by Curt Haltiwanger 04-02-27
# ------------------------------------
# As I write this, the most probable use that occurs to me would be if
someone
# was using the cif to store all of the reflection data as input to the next
# step in the data processing and structure solution process. If that
is the
# case then there are other items that would be interesting, x,y position on
# the detector, frame and angle info, etc. I don't think that is a direction
# that we want to go.
#
# RESPONSE by IDB 04-03-05
#-------------------------
# There is already an image dictionary for reporting the contents of an two-
# dimensional diffraction image. This is written in DDL2 but could be
# converted to DDL1 if there were a demand.
#
# STATUS: Recommend that this item be dropped (unless there is an outcry)
#-----------------------------------------------------
#
##########################################
#
# Item 8
#
##########################################
#
# _geom_bond_multiplicity
#
# 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. This is the way in which bond lengths are
published in
# Acta Cryst.
#
# COMMENT by Howard Flack 04-01-14
# --------------------------------
# OK with me
#
# COMMENT by Curt Haltwanger 04-02-27
# -----------------------------------
# I associate bond multiplicity with single and double bonds. Perhaps
that is
# more correctly referred to as bond order, but multiplicity seems to
have the
# possibility of being confusing. IUPAC defines Multiplicity as "The
existence
# of several degenerate wavefunctions distinguished only by the relative
# orientation of the angular spin momentum. Defined by the total angular
spin
# momentum S, it is given by 2S+1." Whatever that means.
# How about _geom_bond_symm_count instead of _geom_bond_multiplicity
#
# RESPONSE by IDB 04-03-05
# ------------------------
# In the draft dictionary text below I have changed the name to
# _geom_bond_count. It is not necessary to include '_symm' since in almost
# all cases if two bonds have exactly the same length they will be
related by
# symmetry. We will need a corresponding item for angles.
#
data_geom_bond_count
_name '_geom_bond_count'
_category geom_bond
_type numb
_list yes
_list_reference '_geom_bond_atom_site_label_'
loop_
_example
_example_detail
; loop_
_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_geom_bond_distance
_geom_bond_count
Ni1 O1 1.789(3) 4
Ni1 O2 2.134(3) 2
;
'Gives the lengths of the six bonds around Ni1'
_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. This should
not be used if symmetry equivalent bonds are included explicitly
in the list.
;
#
# STATUS: Ready for approval
#
##########################################
#
# Item 9
#
##########################################
#
# Category refine_scattering_density
#
# COMMENT
# -------
# The current dictionary has items that give the maximum and minimum
values of
# the difference scattering density. Users are encouraged to identify the
# positions of the maximum and minimum in a _*_details item.
#
# There are occasions when one might wish to give a list of peaks in an
x-ray,
# electron or neutron scattering density map together with their positions.
# This category is designed to hold this information.
#
# COMMENT from Curt Haltiwanger 04-02-27
# --------------------------------------
# It is important to distinguish between electron density and electron
density
# map peaks. Most programs and their users look only at peaks. Large
regions
# of diffuse electron density (solvent columns and solvent molecules in
large
# holes come to mind) can be very hard to identify and describe. If we are
# going to come up with definitions to describe electron density, we need to
# consider ways to deal with diffuse density.
# I cannot tell from the discussion here so far what information we are
# trying to capture. I thought initially that this would be a way to give
# more details regarding residual difference electron density peaks, but
from
# the definitions difference density peaks are not included at all. Does
# anyone calculate refined scattering density? Is this essentially what
x-ray
# folks would call an electron density map or an Fo map?
# I believe current accepted practice is to calculate a final difference
map.
# It makes sense to me to report the position and height of the largest
peaks
# and holes. I look forward to hearing more discussion of this.
#
# COMMENT from Howard Flack 04-01-14
# ----------------------------------
# It seems to me that you need some more input from the people who
# requested this item to know whether they want full, difference, partial
# difference etc. I don't like the idea of a default radiation probe.
#
# RESPONSE by IDB.
# ----------------
# I cannot recall who asked for this item but there seems to be a sufficient
# number of complications that we should drop this item until we get a clear
# request stating exactly what is needed and why. I have left in the
comments
# that have been made since the previous discussion paper to illustrate some
# of the problems.
#
#data_refine_scattering_density_[]
#_name refine_scattering_density
#_category null
#_type category_overview
#_example
#; loop_
# _refine_scattering_density_id
# _refine_scattering_density_position_x
# _refine_scattering_density_position_y
# _refine_scattering_density_position_z
# _refine_scattering_density_peak
# _refine_scattering_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 scattering density map can be reported. The
#nature of the scattering density is determined by the radiation
#given in _diffrn_radiation_probe.
#;
#
# QUERY
# -----
# _diffrn_radiation_probe is not always given. Should it have a default
value
# of 'x-ray'?
#
# REPLY by Curt Haltiwanger 04-02-27
#--------------------------
# >>>>>>>>>> Is a wavelength always [given] for x-ray experiments?
# >>>>>>>>>> Could the default be determined on the basis of the
wavelength or
# lack thereof?
#
#data_refine_scattering_density_details
#_name '_refine_scattering_density_details'
#_category refine_scattering_density
#_type char
#_list yes
#_list_reference '_refine_scattering_density_details
#loop_ _example 'Probably Mo'
# 'Uncertain peak'
# 'Broad diffuse peak'
#_definition
#; A description of the scattering density peak
#;
#
#data_refine_scattering_density_id
#_name '_refine_scattering_density_id'
#_category refine_scattering_density
#_type char
#_list yes
#_list_mandatory yes
#_example ?
#_definition
#; A code identifying this particular scattering density peak.
#;
#
#
#data_refine_scattering_density_peak
#_name '_refine_scattering_density_peak'
#_category refine_scattering_density
#_type numb
#_list yes
#_list_reference '_refine_scattering_density_id'
#loop_
#_units
#_units_detail
# e.A-3 'electrons per cubic angstrom for x-ray diffraction'
# ? 'for neutron diffraction'
# ? 'for electron diffraction'
# e.A-3 'electrons per cubic angstrom for gamma ray diffraction'
#_example ?
#_definition
#; The measured scattering density at the given position. The
# units are determined by the value of
_diffrn_radiation_probe.
#;
#
#data_refine_scattering_density_position_
#loop_
#_name _refine_scattering_density_position_x
# _refine_scattering_density_position_y
# _refine_scattering_density_position_z
#_category refine_scattering_density
#_type num
#_type_conditions esd
#_list yes
#_list_reference _refine_scattering_density_id
#_example ?
#_definition
#; The positional coordinates in fractions of the unit
cell at
# which the electron density peak occurs.
#;
#
# QUERY: The definitions above imply the full scattering density. Should we
# make provision of the difference density to be given instead or as
well as?
#
# REPLY by Curt 04-02-27
#>>>>>>>>>> I would say yes definitely. I think this is the most likely use
# of such data.
#
# QUERY: Should there be provision for partial difference maps, i.e., maps
# with only some atoms removed? How should this be done?
#
# REPLY by Curt 04-02-27
#>>>>>>>> I don't think this is needed as a separate definition.
# If the cif has a list of atoms and a difference density peaks are reported
# then the difference peaks are what is left. If electron density peaks are
# reported then they should be for all reported atoms plus any big peaks
that
# are in the list. But doesn't this open up another of these things that
# could get out of hand. What about 2Fo - Fc maps? Do we expect the
user to
# report the cut off criteria. I think it goes back to who is going to use
# this for what. For the majority of small molecule scientists, this will
# never get used or will be used only for difference peaks.
#
# STATUS: Recommend this be dropped (unless there is an outcry)
#
#################################
#
# Item 10.
#
#################################
#
# _atomic_sites_solution_hydrogens
#
# COMMENT: The definition of this item in the current dictionary is bundled
# with primary and secondary solution methods
# and for this reason there is no flag to indicate that the hydrogen atoms
# were not located. We need a new flag for this case.
#
# Add to the enumeration loop the following
#
# notdet 'coordinates were not determined'
#
# COMMENT by Howard Flack 04-01-14
# --------------------------------
# OK with me.
#
# STATUS: Ready for approval
#
#####################################
#
# Item 11 Distributed scattering density
#
#####################################
#
# The following items are based on a request from David Watkin and are newly
# introduced into our discussion. They are intended to describe electron
# density (or other scattering density) that is not in the form of a
spherical
# atom, e.g., a ring of density arising 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, but flagged with an
identifier
# that links them to a new category giving details of the shape of the
# distribution. This requires an _*_distributed_density_id item in the
# atom_site category, and the definition of a new distributed_density
# 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 a distributed density defined in the distributed_density
category. Note that all the atoms that give rise to the
distributed density should be included in the atom_site list,
even when they, or the centroid of the distribution, lie on a
special position. The value of
_atom_site_symmetry_multiplicity should be chosen so that the
sum of all the atoms multiplied by their symmetry
multiplicity
equals the chemical formula multiplied by 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,
cylinder or sphere.
;
loop_ _example_detail
_example
;
This is a fictitious (and chemically implausible) example 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 but one quarter of the Cp* molecules are freely rotating, while the
other three quarters occupy fixed positions. 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. 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. Note
that 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 the
_atom_site_symmetry_multiplicity is given. The composition defined in the
atom_site loop is linked to the distributed_density loop through the parent-
child identifiers, 'an1' and 'an2'. The one quarter of the Cp*
molecules that
are rotating have the occupation number 5/6 x 1/4 = 5/24 = 0.208, the
remainder have the occupation number 5/6 x 3/4 = 15/24 = 0.625.
;
;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 scattering
density of the given radius.
;
_definition
; Information about the distribution of scattering 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 direction ratios (in reciprocal lattice units) of the
line of
distributed density or of the axis of the cylindrical shell or
ring of distributed density.
Note that in a non-orthogonal coordinate system the direction
ratios of a line are expressed in terms of the reciprocal
rather than the real lattice.
;
#
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 cylinder of distributed density in
Angstrom units. If this number is set to the translation
repeat in the direction of the axis of the distribution,
it describes an infinite line or cylinder of scattering
density running through the crystal.
;
#
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 cylindrical or spherical shell, or the
radius
of the ring 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 ?
ring ?
cylinder ?
sphere ?
other 'Give details in _distributed_density_details'
_definition
; A flag that indicates the type of distributed density. The
line and ring are one dimensional arrangements of charge and
the cylinder and sphere are two dimensional charge
shells. In
each case the thickness of the distribution is determined by
the scattering factor of the element and 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 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. Note that all
the atoms that give rise to the distributed density should be
listed in the atom_site category even if they, or the
centroid
of the distribution, lie on special positions of high
symmetry.
;
#
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 value of the isotropic atomic displacement parameter
applied to each portion of the distributed density. This
parameter together with the scattering factor of the atoms
whose density is distributed, indicates the thickness of the
line, ring or shell of density.
;
# STATUS: Open for discussion
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