##############################################################################
# #
# Image CIF Dictionary (imgCIF) #
# and Crystallographic Binary File Dictionary (CBF) #
# Extending the Macromolecular CIF Dictionary (mmCIF) #
# #
# Version 1.0 #
# of 2000-12-21 #
# #
# Adapted from the #
# imgCIF Workshop, BNL Oct 1997 #
# and #
# Crystallographic Binary File Format Draft Proposal #
# by Andy Hammersley #
# #
##############################################################################
# #
# First DDL 2.1 Version #
# by #
# John Westbrook #
# Nucleic Acid Database #
# Rutgers University #
# #
##############################################################################
# These revisions by: Herbert J. Bernstein, yaya@bernstein-plus-sons.com #
# Incorporating comments by I. David Brown, John Westbrook and Brian McMahon #
##############################################################################
data_cif_img.dic
_dictionary.title cif_img.dic
_dictionary.version 1.0
_dictionary.datablock_id cif_img.dic
##############################################################################
# CONTENTS
#
# CATEGORY_GROUP_LIST
#
# category ARRAY_DATA
#
# _array_data.array_id
# _array_data.binary_id
# _array_data.data
#
# category ARRAY_ELEMENT_SIZE
#
# _array_element_size.array_id
# _array_element_size.index
# _array_element_size.size
#
# category ARRAY_INTENSITIES
#
# _array_intensities.array_id
# _array_intensities.binary_id
# _array_intensities.gain
# _array_intensities.gain_esd
# _array_intensities.linearity
# _array_intensities.offset
# _array_intensities.scaling
# _array_intensities.overload
# _array_intensities.undefined_value
#
# category ARRAY_STRUCTURE
#
# _array_structure.byte_order
# _array_structure.compression_type
# _array_structure.encoding_type
# _array_structure.id
#
# category ARRAY_STRUCTURE_LIST
#
# _array_structure_list.array_id
# _array_structure_list.dimension
# _array_structure_list.direction
# _array_structure_list.index
# _array_structure_list.precedence
#
# category AXIS
#
# _axis.depends_on
# _axis.equipment
# _axis.id
# _axis.offset[1]
# _axis.offset[2]
# _axis.offset[3]
# _axis.type
# _axis.vector[1]
# _axis.vector[2]
# _axis.vector[3]
#
# category DIFFRN_DETECTOR
#
# _diffrn_detector.details
# _diffrn_detector.detector
# _diffrn_detector.diffrn_id
# _diffrn_detector.dtime
# _diffrn_detector.id
# _diffrn_detector.number_of_axes
# _diffrn_detector.type
#
# category DIFFRN_DETECTOR_AXIS
#
# _diffrn_detector_axis.id
# _diffrn_detector_axis.axis_id
#
# category DIFFRN_DETECTOR_ELEMENT
#
# _diffrn_detector_element.center[1]
# _diffrn_detector_element.center[2]
# _diffrn_detector_element.id
# _diffrn_detector_element.detector_id
#
# category DIFFRN_FRAME_DATA
#
# _diffrn_frame_data.array_id
# _diffrn_frame_data.binary_id
# _diffrn_frame_data.detector_element_id
# _diffrn_frame_data.id
#
# category DIFFRN_MEASUREMENT
#
# _diffrn_measurement.diffrn_id
# _diffrn_measurement.details
# _diffrn_measurement.device
# _diffrn_measurement.device_details
# _diffrn_measurement.device_type
# _diffrn_measurement.id
# _diffrn_measurement.method
# _diffrn_measurement.number_of_axes
# _diffrn_measurement.specimen_support
#
# category DIFFRN_MEASUREMENT_AXIS
#
# _diffrn_measurement_axis.id
# _diffrn_measurement_axis.axis_id
#
# category DIFFRN_REFLN
#
# _diffrn_refln.frame_id
#
# category DIFFRN_SCAN
#
# _diffrn_scan.id
# _diffrn_scan.integration_time
# _diffrn_scan.frame_id_start
# _diffrn_scan.frame_id_end
# _diffrn_scan.frames
#
# category DIFFRN_SCAN_AXIS
#
# _diffrn_scan_axis.scan_id
# _diffrn_scan_axis.axis_id
# _diffrn_scan_axis.angle_start
# _diffrn_scan_axis.angle_range
# _diffrn_scan_axis.angle_increment
# _diffrn_scan_axis.displacement_start
# _diffrn_scan_axis.displacement_range
# _diffrn_scan_axis.displacement_increment
#
# category DIFFRN_SCAN_FRAME
#
# _diffrn_scan_frame.frame_id
# _diffrn_scan_frame.frame_number
# _diffrn_scan_frame.integration_time
# _diffrn_scan_frame.scan_id
#
# category DIFFRN_SCAN_FRAME_AXIS
#
# _diffrn_scan_frame_axis.axis_id
# _diffrn_scan_frame_axis.angle
# _diffrn_scan_frame_axis.displacement
# _diffrn_scan_frame_axis.frame_id
#
# ITEM_TYPE_LIST
# ITEM_UNITS_LIST
# DICTIONARY_HISTORY
#
##############################################################################
#########################
## CATEGORY_GROUP_LIST ##
#########################
loop_
_category_group_list.id
_category_group_list.parent_id
_category_group_list.description
'inclusive_group' .
; Categories that belong to the dictionary extension.
;
'array_data_group'
'inclusive_group'
; Categories that describe array data.
;
'axis_group'
'inclusive_group'
; Categories that describe axes.
;
'diffrn_group'
'inclusive_group'
; Categories that describe details of the diffraction experiment.
;
##############
# ARRAY_DATA #
##############
save_ARRAY_DATA
_category.description
;
Data items in the ARRAY_DATA category are the containers for
the array data items described in category ARRAY_STRUCTURE.
;
_category.id array_data
_category.mandatory_code no
loop_
_category_key.name '_array_data.array_id'
'_array_data.binary_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
This example shows two binary data blocks. The first one
was compressed by the CBF_CANONICAL compression algorithm and
presented as hexadecimal data. The first character "H" on the
data lines means hexadecimal. It could have been "O" for octal
or "D" for decimal. The second character on the line shows
the number of bytes in each word (in this case "4"), which then
requires 8 hexadecimal digits per word. The third character
gives the order of octets within a word, in this case "<"
for the ordering 4321 (i.e. "big-endian"). Alternatively the
character ">" could have been used for the ordering 1234
(i.e. "little-endian"). The block has a "message digest"
to check the integrity of the data.
The second block is similar, but uses CBF_PACKED compression
and BASE64 encoding. Note that the size and the digest are
different.
;
;
loop_
_array_data.array_id
_array_data.binary_id
_array_data.data
image_1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF_CANONICAL"
Content-Transfer-Encoding: X-BASE16
X-Binary-Size: 3927126
X-Binary-ID: 1
Content-MD5: u2sTJEovAHkmkDjPi+gWsg==
# Hexadecimal encoding, byte 0, byte order ...21
#
H4< 0050B810 00000000 00000000 00000000 000F423F 00000000 00000000 ...
....
--CIF-BINARY-FORMAT-SECTION----
;
image_2 2
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF-PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3745758
X-Binary-ID: 1
Content-MD5: 1zsJjWPfol2GYl2V+QSXrw==
ELhQAAAAAAAA...
...
--CIF-BINARY-FORMAT-SECTION----
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_data.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_data.array_id'
_item.category_id array_data
_item.mandatory_code yes
_item_type.code code
save_
save__array_data.binary_id
_item_description.description
; This item is an integer identifier which, along with
_array_data.array_id should uniquely identify the
particular block of array data.
If _array_data.binary_id is not explicitly given,
it defaults to 1.
The value of _array_data.binary_id distinguishes
among multiple sets of data with the same array
structure.
If the MIME header of the data array specifies a
value for X-Binary-Id, these values should be equal.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_data.binary_id' array_data
implicit
'_diffrn_frame_data.binary_id' diffrn_frame_data
implicit
'_array_intensities.binary_id' array_intensities
implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_frame_data.binary_id' '_array_data.binary_id'
'_array_intensities.binary_id' '_array_data.binary_id'
_item_default.value 1
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_data.data
_item_description.description
; The value of _array_data.data contains the array data
encapsulated in a STAR string.
The representation used is a variant on the
Multipurpose Internet Mail Extensions (MIME) specified
in RFC 2045-2049 by N. Freed et al. The boundary
delimiter used in writing an imgCIF or CBF is
"--CIF-BINARY-FORMAT-SECTION--" (including the
required initial "--").
The Content-Type may be any of the discrete types permitted
in RFC 2045; "application/octet-stream" is recommended.
If an octet stream was compressed, the compression should
be specified by the parameter 'conversions="x-CBF_PACKED"'
or the parameter 'conversions="x-CBF_CANONICAL"'.
The Content-Transfer-Encoding may be "BASE-64",
"Quoted-Printable", "X-BASE-8", "X-BASE-10", or
"X-BASE-16" for an imgCIF or "BINARY" for a CBF. The
octal, decimal and hexadecimal transfer encodings are
for convenience in debugging, and are not recommended
for archiving and data interchange.
In an imgCIF file, the encoded binary data begins after
the empty line terminating the header. In a CBF, the
raw binary data begins after an empty line terminating
the header and after the sequence:
Octet Hex Decimal Purpose
0 0C 12 (ctrl-L) Page break
1 1A 26 (ctrl-Z) Stop listings in MS-DOS
2 04 04 (Ctrl-D) Stop listings in UNIX
3 D5 213 Binary section begins
None of these octets are included in the calculation of
the message size, nor in the calculation of the
message digest.
The X-Binary-Size header specifies the size of the
equivalent binary data in octets. If compression was
used, this size is the size after compression, including
any book-keeping fields. And adjustment is made for
the deprecated binary formats in which 8 bytes of binary
header are used for the compression type. In that case,
the 8 bytes used for the compression type is subtracted
from the size, so that the same size will be reported
if the compression type is supplied in the MIME header.
Use of the MIME header is the recommended way to
supply the compression type. In general, no portion of
the binary header is included in the calculation of the size.
The X-Binary-Element-Type header specifies the type of
binary data in the octets, using the same descriptive
phrases as in _array_structure.encoding_type. The default
value is "unsigned 32-bit integer".
An MD5 message digest may, optionally, be used. The "RSA Data
Security, Inc. MD5 Message-Digest Algorithm" should be used.
No portion of the header is included in the calculation of the
message digest.
If the Transfer Encoding is "X-BASE-8", "X-BASE-10", or
"X-BASE-16", the data is presented as octal, decimal or
hexadecimal data organized into lines or words. Each word
is created by composing octets of data in fixed groups of
2, 3, 4, 6 or 8 octets, either in the order ...4321 ("big-
endian") or 1234... (little-endian). If there are fewer
than the specified number of octets to fill the last word,
then the missing octets are presented as "==" for each
missing octet. Exactly two equal signs are used for each
missing octet even for octal and decimal encoding.
The format of lines is:
rnd xxxxxx xxxxxx xxxxxx
where r is "H", "O", or "D" for hexadecimal, octal or
decimal, n is the number of octets per word. and d is "<"
for ">" for the "...4321" and "1234..." octet orderings
respectively. The "==" padding for the last word should
be on the appropriate side to correspond to the missing
octets, e.g.
H4< FFFFFFFF FFFFFFFF 07FFFFFF ====0000
or
H3> FF0700 00====
For these hex, octal and decimal formats, only, comments
beginning with "#" are permitted to improve readability.
BASE64 encoding follows MIME conventions. Octets are
in groups of three, c1, c2, c3. The resulting 24 bits
are broken into four 6-bit quantities, starting with
the high-order six bits (c1 >> 2) of the first octet, then
the low-order two bits of the first octet followed by the
high-order 4 bits of the second octet ((c1 & 3)<<4 | (c2>>4)),
then the bottom 4 bits of the second octet followed by the
high order two bits of the last octet ((c2 & 15)<<2 | (c3>>6)),
then the bottom six bits of the last octet (c3 & 63). Each
of these four quantities is translated into an ASCII character
using the mapping:
1 2 3 4 5 6
0123456789012345678901234567890123456789012345678901234567890123
| | | | | | |
ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/
With short groups of octets padded on the right with one "="
if c3 is missing, and with "==" if both c2 and c3 are missing.
QUOTED-PRINTABLE encoding also follows MIME conventions, copying
octets without translation if their ASCII values are 32..38,
42, 48..57, 59..60, 62, 64..126 and the octet is not a ";"
in column 1. All other characters are translated to =nn, where
nn is the hexadecimal encoding of the octet. All lines are
"wrapped" with a terminating "=" (i.e. the MIME conventions
for an implicit line terminator are never used).
;
_item.name '_array_data.data'
_item.category_id array_data
_item.mandatory_code yes
_item_type.code binary
save_
######################
# ARRAY_ELEMENT_SIZE #
######################
save_ARRAY_ELEMENT_SIZE
_category.description
;
Data items in the ARRAY_ELEMENT_SIZE category record the physical
size of array elements along each array dimension.
;
_category.id array_element_size
_category.mandatory_code no
loop_
_category_key.name '_array_element_size.array_id'
'_array_element_size.index'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - A regular 2D array with a uniform element dimension
of 1220 nanometres.
;
;
loop_
_array_element_size.array_id
_array_element_size.index
_array_element_size.size
image_1 1 1.22e-6
image_1 2 1.22e-6
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_element_size.array_id
_item_description.description
;
This item is a pointer to _array_structure.id in the
ATOM_STRUCTURE category.
;
_item.name '_array_element_size.array_id'
_item.category_id array_element_size
_item.mandatory_code yes
_item_type.code code
save_
save__array_element_size.index
_item_description.description
;
This item is a pointer to _array_structure_list.index in the
ATOM_STRUCTURE_LIST category.
;
_item.name '_array_element_size.index'
_item.category_id array_element_size
_item.mandatory_code yes
_item_type.code code
save_
save__array_element_size.size
_item_description.description
;
The size in metres of an image element in this
dimension. This supposes that the elements are arranged
on a regular grid.
;
_item.name '_array_element_size.size'
_item.category_id array_element_size
_item.mandatory_code yes
_item_type.code float
_item_units.code 'metres'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
#####################
# ARRAY_INTENSITIES #
#####################
save_ARRAY_INTENSITIES
_category.description
;
Data items in the ARRAY_INTENSITIES category record the
information required to recover the intensity data from
the set of data values stored in the ARRAY_DATA category.
;
_category.id array_intensities
_category.mandatory_code no
loop_
_category_key.name '_array_intensities.array_id'
'_array_intensities.binary_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1
;
;
loop_
_array_intensities.array_id
_array_intensities.linearity
_array_intensities.gain
_array_intensities.overload
_array_intensities.undefined_value
image_1 linear 1.2 655535 0
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_intensities.array_id
_item_description.description
;
This item is a pointer to _array_structure.id in the
ATOM_STRUCTURE category.
;
_item.name '_array_intensities.array_id'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code code
save_
save__array_intensities.binary_id
_item_description.description
; This item is a pointer to _array_data.binary_id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_intensities.binary_id'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code int
save_
save__array_intensities.gain
_item_description.description
;
Detector "gain". The factor by which linearized
intensity values should be divided to produce
counts.
;
_item.name '_array_intensities.gain'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code float
loop_
_item_range.maximum
_item_range.minimum
. 0.0
loop_
_item_related.related_name
_item_related.function_code '_array_intensities.gain_esd'
'associated_value'
save_
save__array_intensities.gain_esd
_item_description.description
;
The estimated standard deviation in detector "gain".
;
_item.name '_array_intensities.gain_esd'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code float
loop_
_item_related.related_name
_item_related.function_code '_array_intensities.gain'
'associated_esd'
save_
save__array_intensities.linearity
_item_description.description
;
The intensity linearity scaling used from raw intensity
to the stored element value:
'linear' is obvious
'offset' means that the value defined by
'_array_intensities.offset' should be added to each
element value.
'scaling' means that the value defined by
'_array_intensities.scaling' should be multiplied with each
element value.
'scaling_offset' is the combination of the two previous cases,
with the scale factor applied before the offset value.
'sqrt_scaled' means that the square root of raw
intensities multiplied by '_array_intensities.scaling' is
calculated and stored, perhaps rounded to the nearest
integer. Thus, linearization involves dividing the stored
values by '_array_intensities.scaling' and squaring the
result.
'logarithmic_scaled' means that the logarithm based 10 of
raw intensities multiplied by '_array_intensities.scaling'
is calculated and stored, perhaps rounded to the nearest
integer. Thus, linearization involves dividing the stored
values by '_array_intensities.scaling' and calculating 10
to the power of this number.
;
_item.name '_array_intensities.linearity'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'linear' .
'offset'
;
The value defined by '_array_intensities.offset' should
be added to each element value.
;
'scaling'
;
The value defined by '_array_intensities.scaling' should be
multiplied with each element value.
;
'scaling_offset'
;
The combination of the scaling and offset
with the scale factor applied before the offset value.
;
'sqrt_scaled'
;
The square root of raw intensities multiplied by
'_array_intensities.scaling' is calculated and stored,
perhaps rounded to the nearest integer. Thus,
linearization involves dividing the stored
values by '_array_intensities.scaling' and squaring the
result.
;
'logarithmic_scaled'
;
The logarithm based 10 of raw intensities multiplied by
'_array_intensities.scaling' is calculated and stored,
perhaps rounded to the nearest integer. Thus,
linearization involves dividing the stored values by
'_array_intensities.scaling' and calculating 10 to the
power of this number.
;
save_
save__array_intensities.offset
_item_description.description
;
Offset value to add to array element values in the manner
described by item _array_intensities.linearity.
;
_item.name '_array_intensities.offset'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
save__array_intensities.scaling
_item_description.description
;
Multiplicative scaling value to be applied to array data
in the manner described by item _array_intensities.linearity.
;
_item.name '_array_intensities.scaling'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
save__array_intensities.overload
_item_description.description
;
The saturation intensity level for this data array.
;
_item.name '_array_intensities.overload'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
save__array_intensities.undefined_value
_item_description.description
;
A value to be substituted for undefined values in
the data array.
;
_item.name '_array_intensities.undefined_value'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
###################
# ARRAY_STRUCTURE #
###################
save_ARRAY_STRUCTURE
_category.description
;
Data items in the ARRAY_STRUCTURE category record the organization and
encoding of array data which may be stored in the ARRAY_DATA category.
;
_category.id array_structure
_category.mandatory_code no
_category_key.name '_array_structure.id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
loop_
_array_structure.id
_array_structure.encoding_type
_array_structure.compression_type
_array_structure.byte_order
image_1 "unsigned 16-bit integer" none little_endian
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_structure.byte_order
_item_description.description
;
The order of bytes for integer values which require more
than 1-byte.
(IBM-PC's and compatibles, and Dec-Vaxes use low-byte-first
ordered integers, whereas Hewlett Packard 700
series, Sun-4 and Silicon Graphics use high-byte-first
ordered integers. Dec-Alphas can produce/use either
depending on a compiler switch.)
;
_item.name '_array_structure.byte_order'
_item.category_id array_structure
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'big_endian'
;
The first byte in the byte stream of the bytes which make up an
integer value is the most significant byte of an integer.
;
'little_endian'
;
The last byte in the byte stream of the bytes which make up an
integer value is the most significant byte of an integer.
;
save_
save__array_structure.compression_type
_item_description.description
;
Type of data compression method used to compress the array
data.
;
_item.name '_array_structure.compression_type'
_item.category_id array_structure
_item.mandatory_code no
_item_type.code code
_item_default.value 'none'
loop_
_item_enumeration.value
_item_enumeration.detail
'none'
;
Data are stored in normal format as defined by
_array_structure.encoding_type and _array_structure.byte_order .
;
'byte_offsets'
;
Using the compression scheme defined in CBF definition
Section 5.0.
;
'packed'
;
Using the 'packed' compression scheme, a CCP4-style packing
(CBFlib section 3.3.2)
;
'canonical'
;
Using the 'canonical' compression scheme (CBFlib section
3.3.1)
;
save_
save__array_structure.encoding_type
_item_description.description
;
Data encoding of a single element of array data.
In several cases, the IEEE format is referenced.
See "IEEE Standard for Binary Floating-Point Arithmetic",
ANSI/IEEE Std 754-1985, the Institute of Electrical and
Electronics Engineers, Inc., NY 1985.
;
_item.name '_array_structure.encoding_type'
_item.category_id array_structure
_item.mandatory_code yes
_item_type.code uline
loop_
_item_enumeration.value
'unsigned 8-bit integer'
'signed 8-bit integer'
'unsigned 16-bit integer'
'signed 16-bit_integer'
'unsigned 32-bit integer'
'signed 32-bit integer'
'signed 32-bit real IEEE'
'signed 64-bit real IEEE'
'signed 32-bit complex IEEE'
save_
save__array_structure.id
_item_description.description
; The value of _array_structure.id must uniquely identify
each item of array data.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure.id' array_structure yes
'_array_data.array_id' array_data yes
'_array_structure_list.array_id' array_structure_list yes
'_array_intensities.array_id' array_intensities yes
'_diffrn_frame_data.array_id' diffrn_frame_data yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_data.array_id' '_array_structure.id'
'_array_structure_list.array_id' '_array_structure.id'
'_array_intensities.array_id' '_array_structure.id'
'_diffrn_frame_data.array_id' '_array_structure.id'
save_
########################
# ARRAY_STRUCTURE_LIST #
########################
save_ARRAY_STRUCTURE_LIST
_category.description
;
Data items in the ARRAY_STRUCTURE_LIST category record the size
and organization of each array dimension.
;
_category.id array_structure_list
_category.mandatory_code no
loop_
_category_key.name '_array_structure_list.array_id'
'_array_structure_list.index'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - An image array of 1300 x 1200 elements. The raster
order of the image is left-to-right (increasing) in
first dimension and bottom-to-top (decreasing) in
the second dimension.
;
;
loop_
_array_structure_list.array_id
_array_structure_list.index
_array_structure_list.dimension
_array_structure_list.precedence
_array_structure_list.direction
image_1 1 1300 1 increasing
image_1 2 1200 2 decreasing
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_structure_list.array_id
_item_description.description
;
This item is a pointer to _array_structure.id in the
ATOM_STRUCTURE category.
;
_item.name '_array_structure_list.array_id'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code code
save_
save__array_structure_list.dimension
_item_description.description
;
The number of elements stored in the array structure in this
dimension.
;
_item.name '_array_structure_list.dimension'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_structure_list.direction
_item_description.description
;
Identifies the direction in which this array index changes.
;
_item.name '_array_structure_list.direction'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code int
loop_
_item_enumeration.value
_item_enumeration.detail
'increasing'
;
Indicates the index changes from 1 to the maximum dimension.
;
'decreasing'
;
Indicates the index changes from the maximum dimension to 1.
;
save_
save__array_structure_list.index
_item_description.description
;
Identifies the one-based index of the row or column in the
array structure.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure_list.index' array_structure_list yes
'_array_structure_list.precedence' array_structure_list yes
'_array_element_size.index' array_element_size yes
_item_type.code int
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_element_size.index' '_array_structure_list.index'
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_structure_list.precedence
_item_description.description
;
Identifies the rank order in which this array index changes
with respect to other array indices. The precedence of 1
indicates the index which changes fastest.
;
_item.name '_array_structure_list.precedence'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
########
# AXIS #
########
save_AXIS
_category.description
;
Data items in the AXIS category record the information required
to describe the various goniometer, detector, source and other
axes needed to specify a data collection. The location of each
axis is specified by two vectors: the axis itself, given as a unit
vector, and an offset to the base of the unit vector. These vectors
are referenced to a right-handed laboratory coordinate system with
its origin in the sample or specimen:
| Y (to complete right-handed system)
|
|
|
|
|
|________________X
/ principal goniometer axis
/
/
/
/
/Z (to source)
Axis 1 (X): The X-axis is aligned to the mechanical axis pointing from
the sample or specimen along the principal axis of the goniometer.
Axis 2 (Y): The Y-axis completes an orthogonal right-handed system
defined by the X-axis and the Z-axis (see below).
Axis 3 (Z): The Z-axis is derived from the source axis which goes from
the sample to the source. The Z-axis is the component of the source axis
in the direction of the source orthogonal to the X-axis in the plane
defined by the X-axis and the source axis.
These axes are based on the goniometer, not on the orientation of the
detector, gravity, etc. The vectors necessary to specify all other
axes are given by sets of three components in the order (X, Y, Z).
If the axis involved is a rotation axis, it is right handed, i.e. as
one views the object to be rotated from the origin (the tail) of the
unit vector, the rotation is clockwise. If a translation axis is
specified, the direction of the unit vector specifies the sense of
positive translation.
All rotations are given in degrees and all translations are given in mm.
Axes may be dependent on one another. The X-axis is the only goniometer
axis the direction of which is strictly connected to the hardware. All
other axes are specified by the positions they would assume when the
axes upon which they depend are at their zero points.
When specifying detector axes, the axis is given to the beam center.
The location of the beam center on the detector should be given in the
DIFFRN_DETECTOR category in distortion-corrected mm from the (0,0) corner
of the detector.
It should be noted that many different origins arise in the definition
of an experiment. In particular, as noted above, we need to specify the
location of the beam center on the detector in terms of the origin of the
detector, which is, of course, not coincident with the center of the
sample.
;
_category.id axis
_category.mandatory_code no
loop_
_category_key.name '_axis.id'
'_axis.equipment'
loop_
_category_group.id 'inclusive_group'
'axis_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
This example shows the axis specification of the axes of a kappa
geometry goniometer (See "X-Ray Structure Determination, A Practical
Guide", 2nd ed. by G. H. Stout, L. H. Jensen, Wiley Interscience,
1989, 453 pp, p 134.).
There are three axes specified, and no offsets. The outermost axis,
omega, is pointed along the X-axis. The next innermost axis, kappa,
is at a 50 degree angle to the X-axis, pointed away from the source.
The innermost axis, phi, aligns with the X-axis when omega and
phi are at their zero-points. If T-omega, T-kappa and T-phi
are the transformation matrices derived from the axis settings,
the complete transformation would be:
x' = (T-omega) (T-kappa) (T-phi) x
;
;
loop_
_axis.id
_axis.type
_axis.equipment
_axis.depends_on
_axis.vector[1] _axis.vector[2] _axis.vector[3]
omega rotation goniometer . 1 0 0
kappa rotation goniometer omega -.64279 0 -.76604
phi rotation goniometer kappa 1 0 0
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 -
This example show the axis specification of the axes of a
detector, source and gravity. We have juggled the order as a
reminder that the ordering of presentation of tokens is not
significant. We have taken the center of rotation of the detector
to be 68 millimetres in the direction away from the source.
;
;
loop_
_axis.id
_axis.type
_axis.equipment
_axis.depends_on
_axis.vector[1] _axis.vector[2] _axis.vector[3]
_axis.offset[1] _axis.offset[2] _axis.offset[3]
source . source . 0 0 1 . . .
gravity . gravity . 0 -1 0 . . .
tranz translation detector rotz 0 0 1 0 0 -68
twotheta rotation detector . 1 0 0 . . .
roty rotation detector twotheta 0 1 0 0 0 -68
rotz rotation detector roty 0 0 1 0 0 -68
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__axis.depends_on
_item_description.description
; The value of _axis.type specifies the next outermost
axis upon which this axis depends.
This item is a pointer to axis.id in the same category.
;
_item.name '_axis.depends_on'
_item.category_id axis
_item.mandatory_code no
save_
save__axis.equipment
_item_description.description
; The value of _axis.type specifies the type of equipment
using the axis: goniometer, detector, gravity, source
or general
;
_item.name '_axis.equipment'
_item.category_id axis
_item.mandatory_code no
_item_type.code ucode
_item_default.value general
loop_
_item_enumeration.value
_item_enumeration.detail goniometer
'equipment used to orient or position samples'
detector
'equipment used to detect reflections'
general
'equipment used for general purposes'
gravity
'axis specifying the downward direction'
source
'axis specifying the direction sample to source'
save_
save__axis.offset[1]
_item_description.description
; The [1] element of the 3-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres
;
_item.name '_axis.offset[1]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.offset[2]
_item_description.description
; The [2] element of the 3-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres
;
_item.name '_axis.offset[2]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.offset[3]
_item_description.description
; The [3] element of the 3-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres
;
_item.name '_axis.offset[3]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.id
_item_description.description
; The value of _axis.id must uniquely identify
each axis relevant to the experiment. Note that multiple
pieces of equipment may share the same axis (e.g. a twotheta
arm), so that the category key for AXIS also includes the
equipment.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_axis.id' axis yes
'_diffrn_detector_axis.axis_id' diffrn_detector_axis yes
'_diffrn_measurement_axis.axis_id' diffrn_measurement_axis yes
'_diffrn_scan_axis.axis_id' diffrn_scan_axis yes
'_diffrn_scan_frame_axis.axis_id' diffrn_scan_frame_axis yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_axis.depends_on' '_axis.id'
'_diffrn_detector_axis.axis_id' '_axis.id'
'_diffrn_measurement_axis.axis_id' '_axis.id'
'_diffrn_scan_axis.axis_id' '_axis.id'
'_diffrn_scan_frame_axis.axis_id' '_axis.id'
save_
save__axis.type
_item_description.description
; The value of _axis.type specifies the type of
axis: rotation, translation (or general when the type is
not relevant, as for gravity)
;
_item.name '_axis.type'
_item.category_id axis
_item.mandatory_code no
_item_type.code ucode
_item_default.value general
loop_
_item_enumeration.value
_item_enumeration.detail rotation
'right-handed axis of rotation'
translation
'translation in the direction of the axis'
general
'axis for which the type is not relevant'
save_
save__axis.vector[1]
_item_description.description
; The [1] element of the 3-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector, and
is dimensionless.
;
_item.name '_axis.vector[1]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__axis.vector[2]
_item_description.description
; The [2] element of the 3-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector, and
is dimensionless.
;
_item.name '_axis.vector[2]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__axis.vector[3]
_item_description.description
; The [3] element of the 3-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector, and
is dimensionless.
;
_item.name '_axis.vector[3]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
##########################################################################
# The following is a restatement of the mmCIF DIFFRN_DETECTOR and #
# DIFFRN_MEASUREMENT categories, modified for the CBF/imgCIF extensions #
##########################################################################
###################
# DIFFRN_DETECTOR #
###################
save_DIFFRN_DETECTOR
_category.description
; Data items in the DIFFRN_DETECTOR category describe the
detector used to measure the scattered radiation, including
any analyser and post-sample collimation.
;
_category.id diffrn_detector
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector.diffrn_id'
'_diffrn_detector.id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_diffrn_detector.diffrn_id 'd1'
_diffrn_detector.detector 'multiwire'
_diffrn_detector.type 'Siemens'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_detector.details
_item_description.description
; A description of special aspects of the radiation detector.
;
_item.name '_diffrn_detector.details'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_detector_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; Need new example here.
;
save_
save__diffrn_detector.detector
_item_description.description
; The general class of the radiation detector.
;
_item.name '_diffrn_detector.detector'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version '_diffrn_radiation_detector'
cifdic.c91
1.0
'_diffrn_detector'
cif_core.dic
2.0
_item_type.code text
loop_
_item_examples.case 'photographic film'
'scintillation counter'
'CCD plate'
'BF~3~ counter'
save_
save__diffrn_detector.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
The value of _diffrn.id uniquely defines a set of
diffraction data.
;
_item.name '_diffrn_detector.diffrn_id'
_item.mandatory_code yes
save_
save__diffrn_detector.dtime
_item_description.description
; The deadtime in microseconds of the detectors used to measure
the diffraction intensities.
;
_item.name '_diffrn_detector.dtime'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version '_diffrn_radiation_detector_dtime'
cifdic.c91
1.0
'_diffrn_detector_dtime'
cif_core.dic
2.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code microseconds
save_
save__diffrn_detector.id
_item_description.description
;
The value of _diffrn_detector.id must uniquely identify
each detector used to collect each diffraction data set.
If the value of _diffrn_detector.id is not given, it is
implicitly equal to the value of _diffrn_detector.diffrn_id
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_detector.id' diffrn_detector implicit
'_diffrn_detector_axis.id' diffrn_detector_axis yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_detector_axis.id' '_diffrn_detector.id'
_item_type.code code
save_
save__diffrn_detector.number_of_axes
_item_description.description
;
The value of _diffrn_detector.number_of_axes gives the
number of axes of the positioner for the detector identified
by _diffrn_detector.id
The word "positioner" is a general term used in instrumentation
design for devices that are used to change the positions of
portions of apparatus by linear translation, rotation, or
combinations of such motions.
The description of each axis should be provided by entries
in DIFFRN_DETECTOR_AXIS.
;
_item.name '_diffrn_detector.number_of_axes'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
save__diffrn_detector.type
_item_description.description
; The make, model or name of the detector device used.
;
_item.name '_diffrn_detector.type'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_detector_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
########################
# DIFFRN_DETECTOR_AXIS #
########################
save_DIFFRN_DETECTOR_AXIS
_category.description
;
Data items in the DIFFRN_DETECTOR_AXIS category associate
axes with detectors.
;
_category.id diffrn_detector_axis
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector_axis.id'
'_diffrn_detector_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_detector_axis.id
_item_description.description
;
This data item is a pointer to _diffrn_detector.id in
the DIFFRN_DETECTOR category.
;
_item.name '_diffrn_detector_axis.id'
_item.category_id diffrn_detector_axis
_item.mandatory_code yes
save_
save__diffrn_detector_axis.axis_id
_item_description.description
;
This data item is a pointer to _axis.id in
the AXIS category.
;
_item.name '_diffrn_detector_axis.axis_id'
_item.category_id diffrn_detector_axis
_item.mandatory_code yes
_item_type.code code
save_
###########################
# DIFFRN_DETECTOR_ELEMENT #
###########################
save_DIFFRN_DETECTOR_ELEMENT
_category.description
;
Data items in the DIFFRN_DETECTOR_ELEMENT category record
the details about spatial layout and other characteristics
of each element of a detector which may have multiple elements.
DRAFT NOTE:
This category is intended to hold definitions which are
specific to the elements of area/array detectors. Generic
features about the detector class are defined in the existing
mmCIF category DIFFRN_DETECTOR.
;
_category.id diffrn_detector_element
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector_element.id'
'_diffrn_detector_element.detector_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - Detector d1 is composed of four CCD detector elements,
each 200 mm by 200 mm, arranged in a square. in the pattern
1 2
*
3 4
Note that the beam center is slightly off of each of the
detector elements, just beyond the lower right corner of 1,
the lower left corner of 2, the upper right corner of 3 and
the upper left corner of 4.
;
;
loop_
_diffrn_detector_element.id
_diffrn_detector_element.detector_id
_diffrn_detector_element.center[1]
_diffrn_detector_element.center[2]
d1 d1_ccd_1 201.5 -1.5
d1 d1_ccd_2 -1.8 -1.5
d1 d1_ccd_3 201.6 201.4
d1 d1_ccd_4 -1.7 201.5
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_detector_element.center[1]
_item_description.description
;
The value of _diffrn_detector_element.center[1] is the X
component of the distortion-corrected beam-center in mm from the
(0, 0) (lower left) corner of the detector element viewed from
the sample side.
;
_item.name '_diffrn_detector_element.center[1]'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_detector_element.center[2]
_item_description.description
;
The value of _diffrn_detector_element.center[2] is the Y
component of the distortion-corrected beam-center in mm from the
(0, 0) (lower left) corner of the detector element viewed from
the sample side.
;
_item.name '_diffrn_detector_element.center[2]'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_detector_element.id
_item_description.description
;
The value of _diffrn_detector_element.id must uniquely identify
each element of a detector.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_detector_element.id'
diffrn_detector_element
yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_frame_data.detector_element_id'
'_diffrn_detector_element.id'
save_
save__diffrn_detector_element.detector_id
_item_description.description
;
This item is a pointer to _diffrn_detector.id
in the DIFFRN_DETECTOR category.
;
_item.name '_diffrn_detector_element.detector_id'
_item.category_id diffrn_detector_element
_item.mandatory_code yes
_item_type.code code
save_
#####################
# DIFFRN_FRAME_DATA #
#####################
save_DIFFRN_FRAME_DATA
_category.description
;
Data items in the DIFFRN_FRAME_DATA category record
the details about each frame of data.
;
_category.id diffrn_frame_data
_category.mandatory_code no
loop_
_category_key.name '_diffrn_frame_data.id'
'_diffrn_frame_data.detector_element_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - A frame containing data from 4 frame elements.
Each frame element has a common array configuration
'array_1' described in ARRAY_STRUCTURE and related
categories. The data for each detector element is
stored in four groups of binary data in the
ARRAY_DATA category, linked by the array_id and
binary_id
;
;
loop_
_diffrn_frame_data.id
_diffrn_frame_data.detector_element_id
_diffrn_frame_data.array_id
_diffrn_frame_data.binary_id
frame_1 d1_ccd_1 array_1 1
frame_1 d1_ccd_2 array_1 2
frame_1 d1_ccd_3 array_1 3
frame_1 d1_ccd_4 array_1 4
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_frame_data.array_id
_item_description.description
;
This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_diffrn_frame_data.array_id'
_item.category_id diffrn_frame_data
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_frame_data.binary_id
_item_description.description
; This item is a pointer to _array_data.binary_id in the
ARRAY_STRUCTURE category.
;
_item.name '_diffrn_frame_data.binary_id'
_item.category_id diffrn_frame_data
_item.mandatory_code implicit
_item_type.code int
save_
save__diffrn_frame_data.detector_element_id
_item_description.description
;
This item is a pointer to _diffrn_detector_element.id
in the DIFFRN_DETECTOR_ELEMENT category.
;
_item.name '_diffrn_frame_data.detector_element_id'
_item.category_id diffrn_frame_data
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_frame_data.id
_item_description.description
;
The value of _diffrn_frame_data.id must uniquely identify
each complete frame of data.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_frame_data.id' diffrn_frame_data yes
'_diffrn_refln.frame_id' diffrn_refln yes
'_diffrn_scan.frame_id_start' diffrn_scan yes
'_diffrn_scan.frame_id_end' diffrn_scan yes
'_diffrn_scan_frame.frame_id' diffrn_scan_frame yes
'_diffrn_scan_frame_axis.frame_id'
diffrn_scan_frame_axis
yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_refln.frame_id' '_diffrn_frame_data.id'
'_diffrn_scan.frame_id_start' '_diffrn_frame_data.id'
'_diffrn_scan.frame_id_end' '_diffrn_frame_data.id'
'_diffrn_scan_frame.frame_id' '_diffrn_frame_data.id'
'_diffrn_scan_frame_axis.frame_id'
'_diffrn_frame_data.id'
save_
########################
## DIFFRN_MEASUREMENT ##
########################
save_DIFFRN_MEASUREMENT
_category.description
; Data items in the DIFFRN_MEASUREMENT category record details
about the device used to orient and/or position the crystal
during data measurement and the manner in which the diffraction
data were measured.
;
_category.id diffrn_measurement
_category.mandatory_code no
loop_
_category_key.name '_diffrn_measurement.diffrn_id'
'_diffrn_measurement.id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_diffrn_measurement.diffrn_id 'd1'
_diffrn_measurement.device '3-circle camera'
_diffrn_measurement.device_type 'Supper model x'
_diffrn_measurement.device_details 'none'
_diffrn_measurement.method 'omega scan'
_diffrn_measurement.details
; Need new example here
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
_diffrn_measurement.diffrn_id 's1'
_diffrn_measurement.device_type 'Philips PW1100/20 diffractometer'
_diffrn_measurement.method 'theta/2theta (\q/2\q)'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_measurement.device
_item_description.description
; The general class of goniometer or device used to support and
orient the specimen.
;
_item.name '_diffrn_measurement.device'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_device'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case '3-circle camera'
'4-circle camera'
'kappa-geometry camera'
'oscillation camera'
'precession camera'
save_
save__diffrn_measurement.device_details
_item_description.description
; A description of special aspects of the device used to measure
the diffraction intensities.
;
_item.name '_diffrn_measurement.device_details'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_device_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; commercial goniometer modified locally to
allow for 90\% \t arc
;
save_
save__diffrn_measurement.device_type
_item_description.description
; The make, model or name of the measurement device
(goniometer) used.
;
_item.name '_diffrn_measurement.device_type'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_device_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'Supper model q'
'Huber model r'
'Enraf-Nonius model s'
'homemade'
save_
save__diffrn_measurement.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
;
_item.name '_diffrn_measurement.diffrn_id'
_item.mandatory_code yes
save_
save__diffrn_measurement.details
_item_description.description
; A description of special aspects of the intensity measurement.
;
_item.name '_diffrn_measurement.details'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; 440 frames, 0.20 degrees, 150 sec, detector
distance 12 cm, detector angle 22.5 degrees
;
save_
save__diffrn_measurement.id
_item_description.description
;
The value of _diffrn_measurement.id must uniquely identify
the set of mechanical characteristics of the device used to
orient and/or position the sample used during collection
of each diffraction data set.
If the value of _diffrn_measurement.id is not given, it is
implicitly equal to the value of _diffrn_measurement.diffrn_id
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_measurement.id' diffrn_measurement implicit
'_diffrn_measurement_axis.id' diffrn_measurement_axis yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_measurement_axis.id' '_diffrn_measurement.id'
_item_type.code code
save_
save__diffrn_measurement.method
_item_description.description
; Method used to measure intensities.
;
_item.name '_diffrn_measurement.method'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_method'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case 'profile data from theta/2theta (\q/2\q) scans'
save_
save__diffrn_measurement.number_of_axes
_item_description.description
;
The value of _diffrn_measurement.number_of_axes gives the
number of axes of the positioner for the goniometer or
other sample orientation or positioning device identified
by _diffrn_measurement.id
The description of the axes should be provided by entries in
DIFFRN_MEASUREMENT_AXIS.
;
_item.name '_diffrn_measurement.number_of_axes'
_item.category_id diffrn_measurement
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
save__diffrn_measurement.specimen_support
_item_description.description
; The physical device used to support the crystal during data
collection.
;
_item.name '_diffrn_measurement.specimen_support'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_specimen_support'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'glass capillary'
'quartz capillary'
'fiber'
'metal loop'
save_
###########################
# DIFFRN_MEASUREMENT_AXIS #
###########################
save_DIFFRN_MEASUREMENT_AXIS
_category.description
;
Data items in the DIFFRN_MEASUREMENT_AXIS category associate
axes with goniometers.
;
_category.id diffrn_measurement_axis
_category.mandatory_code no
loop_
_category_key.name '_diffrn_measurement_axis.id'
'_diffrn_measurement_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_measurement_axis.id
_item_description.description
;
This data item is a pointer to _diffrn_measurement.id in
the DIFFRN_MEASUREMENT category.
;
_item.name '_diffrn_measurement_axis.id'
_item.category_id diffrn_measurement_axis
_item.mandatory_code yes
save_
save__diffrn_measurement_axis.axis_id
_item_description.description
;
This data item is a pointer to _axis.id in
the AXIS category.
;
_item.name '_diffrn_measurement_axis.axis_id'
_item.category_id diffrn_measurement_axis
_item.mandatory_code yes
_item_type.code code
save_
################
# DIFFRN_REFLN #
################
save_DIFFRN_REFLN
_category.description
;
This category redefinition has been added to extend the key of
the standard DIFFRN_REFLN category.
;
_category.id diffrn_refln
_category.mandatory_code no
_category_key.name '_diffrn_refln.frame_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_refln.frame_id
_item_description.description
;
This item is a pointer to _diffrn_frame_data.id
in the DIFFRN_FRAME_DATA category.
;
_item.name '_diffrn_refln.frame_id'
_item.category_id diffrn_refln
_item.mandatory_code yes
_item_type.code code
save_
###############
# DIFFRN_SCAN #
###############
save_DIFFRN_SCAN
_category.description
;
Data items in the DIFFRN_SCAN category describe the parameters of one
or more scans, relating axis positions to frames.
;
_category.id diffrn_scan
_category.mandatory_code no
_category_key.name '_diffrn_scan.id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - derived from a suggestion by R. M. Sweet.
The vector of each axis is not given here, because it is provided in
the AXIS category. By making _diffrn_scan_axis.scan_id and
_diffrn_scan_axis.axis_id keys of the DIFFRN_SCAN_AXIS category,
an arbitrary number of scanning and fixed axes can be specified for a
scan. We have specified three rotation axes and one translation axis
at non-zero values, with one axis stepping. There is no reason why
more axes could not have been specified to step. We have specified
range information, but note that it is redundant from the number of
frames and the increment, so we could drop the data item
_diffrn_scan_axis.angle_range .
We have specified both the sweep data and the data for a single frame.
;
;
_diffrn_scan.id 1
_diffrn_scan.integration_time 3.0
_diffrn_scan.frame_id_start mad_L2_000
_diffrn_scan.frame_id_end mad_L2_200
_diffrn_scan.frames 201
loop_
_diffrn_scan_axis.scan_id
_diffrn_scan_axis.axis_id
_diffrn_scan_axis.angle_start
_diffrn_scan_axis.angle_range
_diffrn_scan_axis.angle_increment
_diffrn_scan_axis.displacement_start
_diffrn_scan_axis.displacement_range
_diffrn_scan_axis.displacement_increment
1 omega 200.0 20.0 0.1 . . .
1 kappa -40.0 0.0 0.0 . . .
1 phi 127.5 0.0 0.0 . . .
1 tranz . . . 2.3 0.0 0.0
_diffrn_scan_frame.scan_id 1
_diffrn_scan_frame.integration_time 3.0
_diffrn_scan_frame.frame_id mad_L2_018
_diffrn_scan_frame.frame_number 18
loop_
_diffrn_scan_frame_axis.frame_id
_diffrn_scan_frame_axis.axis_id
_diffrn_scan_frame_axis.angle
_diffrn_scan_frame_axis.displacement
mad_L2_018 omega 201.8 .
mad_L2_018 kappa -40.0 .
mad_L2_018 phi 127.5 .
mad_L2_018 tranz . 2.3
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_scan.id
_item_description.description
; The value of _diffrn_scan.id uniquely identifies each
scan. The identifier is used to tie together all the
information about the scan.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_scan.id' diffrn_scan yes
'_diffrn_scan_axis.scan_id' diffrn_scan_axis yes
'_diffrn_scan_frame.scan_id' diffrn_scan_frame yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_scan_axis.scan_id' '_diffrn_scan.id'
'_diffrn_scan_frame.scan_id' '_diffrn_scan.id'
save_
save__diffrn_scan.integration_time
_item_description.description
;
The time in seconds to integrate each step of the scan.
;
_item.name '_diffrn_scan.integration_time'
_item.category_id diffrn_scan
_item.mandatory_code yes
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan.frame_id_start
_item_description.description
;
The value of this data item is the identifier of the
first frame in the scan.
This item is a pointer to _diffrn_frame_data.id in the
DIFFRN_FRAME_DATA category.
;
_item.name '_diffrn_scan.frame_id_start'
_item.category_id diffrn_scan
_item.mandatory_code yes
save_
save__diffrn_scan.frame_id_end
_item_description.description
;
The value of this data item is the identifier of the
last frame in the scan.
This item is a pointer to _diffrn_frame_data.id in the
DIFFRN_FRAME_DATA category.
;
_item.name '_diffrn_scan.frame_id_end'
_item.category_id diffrn_scan
_item.mandatory_code yes
save_
save__diffrn_scan.frames
_item_description.description
;
The value of this data item is the number of frames in
the scan.
;
_item.name '_diffrn_scan.frames'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
. 1
1 1
save_
####################
# DIFFRN_SCAN_AXIS #
####################
save_DIFFRN_SCAN_AXIS
_category.description
;
Data items in the DIFFRN_SCAN_AXIS category describe the settings of
axes for particular scans. Unspecified axes are assumed to be at
their zero points.
;
_category.id diffrn_scan_axis
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_axis.scan_id'
'_diffrn_scan_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_axis.scan_id
_item_description.description
;
The value of this data item is the identifier of the
scan for which axis settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan.id
This item is a pointer to _diffrn_scan.id in the
DIFFRN_SCAN category.
;
_item.name '_diffrn_scan_axis.scan_id'
_item.category_id diffrn_scan_axis
_item.mandatory_code yes
save_
save__diffrn_scan_axis.axis_id
_item_description.description
;
The value of this data item is the identifier of one of
the axes for the scan for which settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan.id .
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_diffrn_scan_axis.axis_id'
_item.category_id diffrn_scan_axis
_item.mandatory_code yes
save_
save__diffrn_scan_axis.angle_start
_item_description.description
;
The starting position for the specified axis in degrees.
;
_item.name '_diffrn_scan_axis.angle_start'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_range
_item_description.description
;
The range from the starting position for the specified axis
in degrees.
;
_item.name '_diffrn_scan_axis.angle_range'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_increment
_item_description.description
;
The increment for each step for the specified axis
in degrees.
;
_item.name '_diffrn_scan_axis.angle_increment'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.displacement_start
_item_description.description
;
The starting position for the specified axis in millimetres.
;
_item.name '_diffrn_scan_axis.displacement_start'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_range
_item_description.description
;
The range from the starting position for the specified axis
in millimetres.
;
_item.name '_diffrn_scan_axis.displacement_range'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_increment
_item_description.description
;
The increment for each step for the specified axis
in millimetres.
;
_item.name '_diffrn_scan_axis.displacement_increment'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
#####################
# DIFFRN_SCAN_FRAME #
#####################
save_DIFFRN_SCAN_FRAME
_category.description
;
Data items in the DIFFRN_SCAN_FRAME category describe the settings of
axes for particular frames. Unspecified axes are assumed to be at
their zero points.
;
_category.id diffrn_scan_frame
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_frame.scan_id'
'_diffrn_scan_frame.frame_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_frame.frame_id
_item_description.description
;
The value of this data item is the identifier of the
frame being examined.
This item is a pointer to _diffrn_frame_data.id in the
DIFFRN_FRAME_DATA category.
;
_item.name '_diffrn_scan_frame.frame_id'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
save_
save__diffrn_scan_frame.frame_number
_item_description.description
;
The value of this data item is the number of the frame within
the scan, starting with 1. It is not necessarily the same as
the value of _diffrn_scan_frame.frame_id, but may be.
;
_item.name '_diffrn_scan_frame.frame_number'
_item.category_id diffrn_scan_frame
_item.mandatory_code no
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
. 0
0 0
save_
save__diffrn_scan_frame.integration_time
_item_description.description
;
The time in seconds to integrate this step of the scan.
;
_item.name '_diffrn_scan_frame.integration_time'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan_frame.scan_id
_item_description.description
; The value of _diffrn_scan_frame.scan_id identifies the scan
containing this frame.
This item is a pointer to _diffrn_scan.id in the
DIFFRN_SCAN category.
;
loop_
_item.name '_diffrn_scan_frame.scan_id'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
save_
##########################
# DIFFRN_SCAN_FRAME_AXIS #
##########################
save_DIFFRN_SCAN_FRAME_AXIS
_category.description
;
Data items in the DIFFRN_SCAN_FRAME_AXIS category describe the settings
of axes for particular frames. Unspecified axes are assumed to be at
their zero points.
;
_category.id diffrn_scan_frame_axis
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_frame_axis.frame_id'
'_diffrn_scan_frame_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_frame_axis.axis_id
_item_description.description
;
The value of this data item is the identifier of one of
the axes for the frame for which settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan_frame.frame_id
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_diffrn_scan_frame_axis.axis_id'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code yes
save_
save__diffrn_scan_frame_axis.angle
_item_description.description
;
The setting of the specified axis in degrees for this frame.
;
_item.name '_diffrn_scan_frame_axis.angle'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.displacement
_item_description.description
;
The setting of the specified axis in millimetres for this
frame
;
_item.name '_diffrn_scan_frame_axis.displacement'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.frame_id
_item_description.description
;
The value of this data item is the identifier of the
frame for which axis settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan_frame.frame_id .
This item is a pointer to _diffrn_frame_data.id in the
DIFFRN_FRAME_DATA category.
;
_item.name '_diffrn_scan_frame_axis.frame_id'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code yes
save_
####################
## ITEM_TYPE_LIST ##
####################
#
#
# The regular expressions defined here are not compliant
# with the POSIX 1003.2 standard as they include the
# '\n' and '\t' special characters. These regular expressions
# have been tested using version 0.12 of Richard Stallman's
# GNU regular expression library in POSIX mode.
# In order to allow presentation of a regular expression
# in a text field concatenate any line ending in a backslash
# with the following line, after discarding the backslash.
#
# A formal definition of the '\n' and '\t' special characters
# is most properly done in the DDL, but for completeness, please
# note that '\n' is the line termination character ('newline')
# and '\t' is the horizontal tab character. There is a formal
# ambiguity in the use of '\n' for line termination, in that
# the intention is that the equivalent machine/OS-dependent line
# termination character sequence should be accepted as a match, e.g.
#
# '\r' (control-M) under MacOS
# '\n' (control-J) under Unix
# '\r\n' (control-M control-J) under DOS and MS Windows
#
loop_
_item_type_list.code
_item_type_list.primitive_code
_item_type_list.construct
_item_type_list.detail
code char
'[_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words ...
;
ucode uchar
'[_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words (case insensitive)
;
line char
'[][ \t_(),.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types / multi-word items ...
;
uline uchar
'[][ \t_(),.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types / multi-word items (case insensitive)
;
text char
'[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
; text item types / multi-line text ...
;
binary char
;\n--CIF-BINARY-FORMAT-SECTION--\n\
[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*}\
\n--CIF-BINARY-FORMAT-SECTION----
;
; binary items are presented as MIME-like ascii-encoded
sections in an imgCIF. In a CBF, raw octet streams
are used to convey the same information.
;
int numb
'-?[0-9]+'
; int item types are the subset of numbers that are the negative
or positive integers.
;
float numb
'-?(([0-9]+)|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)?'
; float item types are the subset of numbers that are the floating
numbers.
;
any char
'.*'
; A catch all for items that may take any form...
;
#####################
## ITEM_UNITS_LIST ##
#####################
loop_
_item_units_list.code
_item_units_list.detail
#
'metres' 'metres'
'centimetres' 'centimetres (metres * 10^( -2))'
'millimetres' 'millimetres (metres * 10^( -3))'
'nanometres' 'nanometres (metres * 10^( -9))'
'angstroms' 'angstroms (metres * 10^(-10))'
'picometres' 'picometres (metres * 10^(-12))'
'femtometres' 'femtometres (metres * 10^(-15))'
#
'reciprocal_metres' 'reciprocal metres (metres * 10^-1)'
'reciprocal_centimetres' 'reciprocal centimetres (metres * 10^( -2)^-1)'
'reciprocal_millimetres' 'reciprocal millimetres (metres * 10^( -3)^-1)'
'reciprocal_nanometres' 'reciprocal nanometres (metres * 10^( -9)^-1)'
'reciprocal_angstroms' 'reciprocal angstroms (metres * 10^(-10)^-1)'
'reciprocal_picometres' 'reciprocal picometres (metres * 10^(-12)^-1)'
#
'nanometres_squared' 'nanometres squared (metres * 10^( -9))^2'
'angstroms_squared' 'angstroms squared (metres * 10^(-10))^2'
'8pi2_angstroms_squared' '8pi^2 * angstroms squared (metres * 10^(-10))^2'
'picometres_squared' 'picometres squared (metres * 10^(-12))^2'
#
'nanometres_cubed' 'nanometres cubed (metres * 10^( -9))^3'
'angstroms_cubed' 'angstroms cubed (metres * 10^(-10))^3'
'picometres_cubed' 'picometres cubed (metres * 10^(-12))^3'
#
'kilopascals' 'kilopascals'
'gigapascals' 'gigapascals'
#
'hours' 'hours'
'minutes' 'minutes'
'seconds' 'seconds'
'microseconds' 'microseconds'
#
'degrees' 'degrees (of arc)'
#
'degrees_per_minute' 'degrees (of arc) per minute'
#
'celsius' 'degrees (of temperature) Celsius'
'kelvins' 'degrees (of temperature) Kelvin'
#
'electrons' 'electrons'
#
'electrons_squared' 'electrons squared'
#
'electrons_per_nanometres_cubed'
; electrons per nanometres cubed (metres * 10^( -9))^3
;
'electrons_per_angstroms_cubed'
; electrons per angstroms cubed (metres * 10^(-10))^3
;
'electrons_per_picometres_cubed'
; electrons per picometres cubed (metres * 10^(-12))^3
;
'kilowatts' 'kilowatts'
'milliamperes' 'milliamperes'
'kilovolts' 'kilovolts'
#
'arbitrary'
; arbitrary system of units.
;
#
loop_
_item_units_conversion.from_code
_item_units_conversion.to_code
_item_units_conversion.operator
_item_units_conversion.factor
###
'metres' 'centimetres' '*' 1.0E+02
'metres' 'millimetres' '*' 1.0E+03
'metres' 'nanometres' '*' 1.0E+09
'metres' 'angstroms' '*' 1.0E+10
'metres' 'picometres' '*' 1.0E+12
'metres' 'femtometres' '*' 1.0E+15
#
'centimetres' 'metres' '*' 1.0E-02
'centimetres' 'millimetres' '*' 1.0E+01
'centimetres' 'nanometres' '*' 1.0E+07
'centimetres' 'angstroms' '*' 1.0E+08
'centimetres' 'picometres' '*' 1.0E+10
'centimetres' 'femtometres' '*' 1.0E+13
#
'millimetres' 'metres' '*' 1.0E-03
'millimetres' 'centimetres' '*' 1.0E-01
'millimetres' 'nanometres' '*' 1.0E+06
'millimetres' 'angstroms' '*' 1.0E+07
'millimetres' 'picometres' '*' 1.0E+09
'millimetres' 'femtometres' '*' 1.0E+12
#
'nanometres' 'metres' '*' 1.0E-09
'nanometres' 'centimetres' '*' 1.0E-07
'nanometres' 'millimetres' '*' 1.0E-06
'nanometres' 'angstroms' '*' 1.0E+01
'nanometres' 'picometres' '*' 1.0E+03
'nanometres' 'femtometres' '*' 1.0E+06
#
'angstroms' 'metres' '*' 1.0E-10
'angstroms' 'centimetres' '*' 1.0E-08
'angstroms' 'millimetres' '*' 1.0E-07
'angstroms' 'nanometres' '*' 1.0E-01
'angstroms' 'picometres' '*' 1.0E+02
'angstroms' 'femtometres' '*' 1.0E+05
#
'picometres' 'metres' '*' 1.0E-12
'picometres' 'centimetres' '*' 1.0E-10
'picometres' 'millimetres' '*' 1.0E-09
'picometres' 'nanometres' '*' 1.0E-03
'picometres' 'angstroms' '*' 1.0E-02
'picometres' 'femtometres' '*' 1.0E+03
#
'femtometres' 'metres' '*' 1.0E-15
'femtometres' 'centimetres' '*' 1.0E-13
'femtometres' 'millimetres' '*' 1.0E-12
'femtometres' 'nanometres' '*' 1.0E-06
'femtometres' 'angstroms' '*' 1.0E-05
'femtometres' 'picometres' '*' 1.0E-03
###
'reciprocal_centimetres' 'reciprocal_metres' '*' 1.0E+02
'reciprocal_centimetres' 'reciprocal_millimetres' '*' 1.0E-01
'reciprocal_centimetres' 'reciprocal_nanometres' '*' 1.0E-07
'reciprocal_centimetres' 'reciprocal_angstroms' '*' 1.0E-08
'reciprocal_centimetres' 'reciprocal_picometres' '*' 1.0E-10
#
'reciprocal_millimetres' 'reciprocal_metres' '*' 1.0E+03
'reciprocal_millimetres' 'reciprocal_centimetres' '*' 1.0E+01
'reciprocal_millimetres' 'reciprocal_nanometres' '*' 1.0E-06
'reciprocal_millimetres' 'reciprocal_angstroms' '*' 1.0E-07
'reciprocal_millimetres' 'reciprocal_picometres' '*' 1.0E-09
#
'reciprocal_nanometres' 'reciprocal_metres' '*' 1.0E+09
'reciprocal_nanometres' 'reciprocal_centimetres' '*' 1.0E+07
'reciprocal_nanometres' 'reciprocal_millimetres' '*' 1.0E+06
'reciprocal_nanometres' 'reciprocal_angstroms' '*' 1.0E-01
'reciprocal_nanometres' 'reciprocal_picometres' '*' 1.0E-03
#
'reciprocal_angstroms' 'reciprocal_metres' '*' 1.0E+10
'reciprocal_angstroms' 'reciprocal_centimetres' '*' 1.0E+08
'reciprocal_angstroms' 'reciprocal_millimetres' '*' 1.0E+07
'reciprocal_angstroms' 'reciprocal_nanometres' '*' 1.0E+01
'reciprocal_angstroms' 'reciprocal_picometres' '*' 1.0E-02
#
'reciprocal_picometres' 'reciprocal_metres' '*' 1.0E+12
'reciprocal_picometres' 'reciprocal_centimetres' '*' 1.0E+10
'reciprocal_picometres' 'reciprocal_millimetres' '*' 1.0E+09
'reciprocal_picometres' 'reciprocal_nanometres' '*' 1.0E+03
'reciprocal_picometres' 'reciprocal_angstroms' '*' 1.0E+01
###
'nanometres_squared' 'angstroms_squared' '*' 1.0E+02
'nanometres_squared' 'picometres_squared' '*' 1.0E+06
#
'angstroms_squared' 'nanometres_squared' '*' 1.0E-02
'angstroms_squared' 'picometres_squared' '*' 1.0E+04
'angstroms_squared' '8pi2_angstroms_squared' '*' 78.9568
#
'picometres_squared' 'nanometres_squared' '*' 1.0E-06
'picometres_squared' 'angstroms_squared' '*' 1.0E-04
###
'nanometres_cubed' 'angstroms_cubed' '*' 1.0E+03
'nanometres_cubed' 'picometres_cubed' '*' 1.0E+09
#
'angstroms_cubed' 'nanometres_cubed' '*' 1.0E-03
'angstroms_cubed' 'picometres_cubed' '*' 1.0E+06
#
'picometres_cubed' 'nanometres_cubed' '*' 1.0E-09
'picometres_cubed' 'angstroms_cubed' '*' 1.0E-06
###
'kilopascals' 'gigapascals' '*' 1.0E-06
'gigapascals' 'kilopascals' '*' 1.0E+06
###
'hours' 'minutes' '*' 6.0E+01
'hours' 'seconds' '*' 3.6E+03
'hours' 'microseconds' '*' 3.6E+09
#
'minutes' 'hours' '/' 6.0E+01
'minutes' 'seconds' '*' 6.0E+01
'minutes' 'microseconds' '*' 6.0E+07
#
'seconds' 'hours' '/' 3.6E+03
'seconds' 'minutes' '/' 6.0E+01
'seconds' 'microseconds' '*' 1.0E+06
#
'microseconds' 'hours' '/' 3.6E+09
'microseconds' 'minutes' '/' 6.0E+07
'microseconds' 'seconds' '/' 1.0E+06
###
'celsius' 'kelvins' '-' 273.0
'kelvins' 'celsius' '+' 273.0
###
'electrons_per_nanometres_cubed'
'electrons_per_angstroms_cubed' '*' 1.0E-03
'electrons_per_nanometres_cubed'
'electrons_per_picometres_cubed' '*' 1.0E-09
#
'electrons_per_angstroms_cubed'
'electrons_per_nanometres_cubed' '*' 1.0E+03
'electrons_per_angstroms_cubed'
'electrons_per_picometres_cubed' '*' 1.0E-06
#
'electrons_per_picometres_cubed'
'electrons_per_nanometres_cubed' '*' 1.0E+09
'electrons_per_picometres_cubed'
'electrons_per_angstroms_cubed' '*' 1.0E+06
###
########################
## DICTIONARY_HISTORY ##
########################
loop_
_dictionary_history.version
_dictionary_history.update
_dictionary_history.revision
1.0 2000-12-21
;
Release version - few typos and tidying up (BM & HJB)
+ Move ITEM_TYPE_LIST, ITEM_UNITS_LIST and DICTIONARY_HISTORY to end
of dictionary.
+ Alphabetize dictionary.
;
0.7.1 2000-09-29
;
Cleanup fixes (JW)
+ Correct spelling of diffrn_measurement_axis in _axis.id
+ Correct ordering of uses of _item.mandatory_code and _item_default.value
;
0.7.0 2000-09-09
;
Respond to comments by I. David Brown (HJB)
+ Added further comments on '\n' and '\t'
+ Updated ITEM_UNITS_LIST by taking section from mmCIF dictionary
and adding metres. Changed all spelling 'meter' to 'metre' throughout.
+ Added missing enumerations to _array_structure.compression_type
and made 'none' the default.
+ Removed parent-child relationship between _array_structure_list.index
and _array_structure_list.precedence .
+ Improve alphabetization.
+ Fix _array_intensities_gain.esd related function.
+ Improved comments in AXIS.
+ Fixed DIFFRN_FRAME_DATA example.
+ Removed erroneous DIFFRN_MEASUREMENT example.
+ Added _diffrn_measurement_axis.id to the category key.
;
0.6.0 1999-01-14
;
Remove redundant information for ENC_NONE data (HJB)
+ After the D5 remove binary section identifier, size and
compression type.
+ Add Control-L to header.
;
0.5.1 1999-01-03
;
Cleanup of typos and syntax errors (HJB)
+ Cleanup example details for DIFFRN_SCAN category.
+ Add missing quote marks for _diffrn_scan.id definition.
;
0.5 1999-01-01
;
Modifications for axis definitions and reduction of binary header (HJB)
+ Restored _diffrn_detector.diffrn_id to DIFFRN_DETECTOR KEY.
+ Added AXIS category.
+ Brought complete DIFFRN_DETECTOR and DIFFRN_MEASUREMENT categories
in from cif_mm.dic for clarity.
+ changed _array_structure.encoding_type from type code to uline and
added X-Binary-Element-Type to MIME header.
+ added detector beam center _diffrn_detector_element.center[1] and
_diffrn_detector_element.center[2]
+ corrected item name of _diffrn_refln.frame_id
+ replace reference to _array_intensities.undefined by
_array_intensities.undefined_value
+ replace references to _array_intensity.scaling with
_array_intensities.scaling
+ added DIFFRN_SCAN... categories
;
0.4 1998-08-11
;
Modifications to the 0.3 imgCIF draft (HJB)
+ Reflowed comment lines over 80 characters and corrected typos.
+ Updated examples and descriptions of MIME encoded data.
+ Change name to cbfext98.dic.
;
0.3 1998-07-04
;
Modifications for imgCIF (HJB)
+ Added binary type, which is a text field containing a variant on
MIME encoded data.
+ Changed type of _array_data.data to binary and specified internal
structure of raw binary data.
+ Added _array_data.binary_id, and made
_diffrn_frame_data.binary_id and _array_intensities.binary_id
into pointers to this item.
;
0.2 1997-12-02
;
Modifications to the CBF draft (JW):
+ Added category hierarchy for describing frame data developed from
discussions at the BNL imgCIF Workshop Oct 1997. The following
changes were made in implementing the workshop draft. Category
DIFFRN_ARRAY_DATA was renamed to DIFFRN_FRAME_DATA. Category
DIFFRN_FRAME_TYPE was renamed to DIFFRN_DETECTOR_ELEMENT. The
parent item for _diffrn_frame_data.array_id was changed from
array_structure_list.array_id to array_structure.id. Item
_diffrn_detector.array_id was deleted.
+ Added data item _diffrn_frame_data.binary_id to identify data groups
within a binary section. The formal identification of the binary section
is still fuzzy.
;
0.1 1997-01-24
;
First draft of this dictionary in DDL 2.1 compliant format by John
Westbrook (JW). This version was adapted from the Crystallographic
Binary File (CBF) Format Draft Proposal provided by Andy Hammersley (AH).
Modifications to the CBF draft (JW):
+ In this version the array description has been cast in the categories
ARRAY_STRUCTURE and ARRAY_STRUCTURE_LIST. These categories have been
generalized to describe array data of arbitrary dimension.
+ Array data in this description are contained in the category ARRAY_DATA.
This departs from the CBF notion of data existing in some special comment.
In this description, data is handled as an ordinary data item encapsulated
in a character data type. Although handling binary data this manner
deviates from CIF conventions, it does not violate any DDL 2.1 rules.
DDL 2.1 regular expressions can be used to define the binary
representation which will permit some level of data validation. In
this version, the placeholder type code "any" has been used.
This translates to a regular expression which will match any pattern.
It should be noted that DDL 2.1 already supports array data objects
although these have not been used in the current mmCIF dictionary. It
may be possible to use the DDL 2.1 ITEM_STRUCTURE and ITEM_STRUCTURE_LIST
categories to provide the information that is carried in by the
ARRAY_STRUCTURE and ARRAY_STRUCTURE_LIST. By moving the array
structure to the DDL level it would be possible to define an array
type as well as a regular expression defining the data format.
+ Multiple array sections can be properly handled within a single datablock.
;
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