############################################################################## # # # Image CIF Dictionary (imgCIF) # # and Crystallographic Binary File Dictionary (CBF) # # Extending the Macromolecular CIF Dictionary (mmCIF) # # # # Version 1.4_DRAFT # # of 2006-07-04 # # ################################################################### # # # *** WARNING *** THIS IS A DRAFT FOR DISCUSSSION *** WARNING *** # # # # SUBJECT TO CHANGE WITHOUT NOTICE # # # # VERSIONS WILL BE POSTED AS cif_img_1.4_DDMMMYY_draft.html # # # # SEND COMMENTS TO imgcif-l@iucr.org CITING THE VERSION # # # ################################################################### # # This draft edited by H. J. Bernstein # # # # by Andrew P. Hammersley, Herbert J. Bernstein and John D. Westbrook # # # # This dictionary was adapted from format discussed at the imgCIF Workshop, # # held at BNL Oct 1997 and the Crystallographic Binary File Format Draft # # Proposal by Andrew Hammersley. The first DDL 2.1 Version was created by # # John Westbrook. This version was drafted by Herbert J. Bernstein and # # incorporates comments by I. David Brown, John Westbrook, Brian McMahon, # # Bob Sweet, Paul Ellis, Harry Powell, Wilfred Li, Gotzon Madariaga, # # Frances C. Bernstein, Chris Nielsen, Nicola Ashcroft and others. # ############################################################################## data_cif_img.dic _dictionary.title cif_img.dic _dictionary.version 1.4_DRAFT _dictionary.datablock_id cif_img.dic ############################################################################## # CONTENTS # # CATEGORY_GROUP_LIST # SUB_CATEGORY # # 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 # _array_intensities.pixel_fast_bin_size # _array_intensities.pixel_slow_bin_size # _array_intensities.pixel_binning_method # # 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.axis_set_id # _array_structure_list.array_id # _array_structure_list.dimension # _array_structure_list.direction # _array_structure_list.index # _array_structure_list.precedence # # category ARRAY_STRUCTURE_LIST_AXIS # # _array_structure_list_axis.axis_id # _array_structure_list_axis.axis_set_id # _array_structure_list_axis.angle # _array_structure_list_axis.angle_increment # _array_structure_list_axis.displacement # _array_structure_list_axis.displacement_increment # _array_structure_list_axis.angular_pitch # _array_structure_list_axis.radial_pitch # # 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_DATA_FRAME # # _diffrn_data_frame.array_id # _diffrn_data_frame.binary_id # _diffrn_data_frame.detector_element_id # _diffrn_data_frame.id # _diffrn_data_frame.details # # 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.axis_id # _diffrn_detector_axis.detector_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_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.axis_id # _diffrn_measurement_axis.measurement_device # _diffrn_measurement_axis.measurement_id # # category DIFFRN_RADIATION # # _diffrn_radiation.collimation # _diffrn_radiation.diffrn_id # _diffrn_radiation.div_x_source # _diffrn_radiation.div_y_source # _diffrn_radiation.div_x_y_source # _diffrn_radiation.filter_edge' # _diffrn_radiation.inhomogeneity # _diffrn_radiation.monochromator # _diffrn_radiation.polarisn_norm # _diffrn_radiation.polarisn_ratio # _diffrn_radiation.polarizn_source_norm # _diffrn_radiation.polarizn_source_ratio # _diffrn_radiation.probe # _diffrn_radiation.type # _diffrn_radiation.xray_symbol # _diffrn_radiation.wavelength_id # # category DIFFRN_REFLN # # _diffrn_refln.frame_id # # category DIFFRN_SCAN # # _diffrn_scan.id # _diffrn_scan.date_end # _diffrn_scan.date_start # _diffrn_scan.integration_time # _diffrn_scan.frame_id_start # _diffrn_scan.frame_id_end # _diffrn_scan.frames # # category DIFFRN_SCAN_AXIS # # _diffrn_scan_axis.axis_id # _diffrn_scan_axis.angle_start # _diffrn_scan_axis.angle_range # _diffrn_scan_axis.angle_increment # _diffrn_scan_axis.angle_rstrt_incr # _diffrn_scan_axis.displacement_start # _diffrn_scan_axis.displacement_range # _diffrn_scan_axis.displacement_increment # _diffrn_scan_axis.displacement_rstrt_incr # _diffrn_scan_axis.scan_id # # category DIFFRN_SCAN_FRAME # # _diffrn_scan_frame.date # _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.angle_increment # _diffrn_scan_frame_axis.angle_rstrt_incr # _diffrn_scan_frame_axis.displacement # _diffrn_scan_frame_axis.displacement_increment # _diffrn_scan_frame_axis.displacement_rstrt_incr # _diffrn_scan_frame_axis.frame_id # # ***DEPRECATED*** data items # # _diffrn_detector_axis.id # _diffrn_measurement_axis.id # # ***DEPRECATED*** category DIFFRN_FRAME_DATA # # _diffrn_frame_data.array_id # _diffrn_frame_data.binary_id # _diffrn_frame_data.detector_element_id # _diffrn_frame_data.id # _diffrn_frame_data.details # # # 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. ; ################## ## SUB_CATEGORY ## ################## loop_ _sub_category.id _sub_category.description 'matrix' ; The collection of elements of a matrix. ; 'vector' ; The collection of elements of a vector. ; ############## # ARRAY_DATA # ############## save_ARRAY_DATA _category.description ; Data items in the ARRAY_DATA category are the containers for the array data items described in the 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 is 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 eight 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: 2 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, the value of _array_data.binary_id should be equal to the value given for X-Binary-ID. ; loop_ _item.name _item.category_id _item.mandatory_code '_array_data.binary_id' array_data implicit '_diffrn_data_frame.binary_id' diffrn_data_frame implicit '_array_intensities.binary_id' array_intensities implicit loop_ _item_linked.child_name _item_linked.parent_name '_diffrn_data_frame.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 '\n--CIF-BINARY-FORMAT-SECTION--' (including the required initial '\n--'). 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 'BASE64', 'Quoted-Printable', 'X-BASE8', 'X-BASE10', 'X-BASE16' or 'X-BASE32K', for an imgCIF or 'BINARY' for a CBF. The octal, decimal and hexadecimal transfer encodings are provided for convenience in debugging and are not recommended for archiving and data interchange. In a CIF, one of the parameters 'charset=us-ascii', 'charset=utf-8' or 'charset=utf-16' may be used on the Content-Transfer-Encoding to specify the character set used for the external presentation of the encoded data. If no charset parameter is given, the character set of the enclosing CIF is assumed. In any case, if a BOM flag is detected (FE FF for big-endian UTF-16, FF FE for little-endian UTF-16 or EF BB BF for UTF-8) is detected, the indicated charset will be assumed until the end of the encoded data or the detection of a different BOM. The charset of the Content-Transfer-Encoding is not the character set of the encoded data, only the character set of the presentation of the encoded data and should be respecified for each distinct STAR string. In an imgCIF file, the encoded binary data begins after the empty line terminating the header. In an imgCIF file, the encoded binary data ends with the terminating boundary delimiter '\n--CIF-BINARY-FORMAT-SECTION----' in the currently effective charset or with the '\n; ' that terminates the STAR string. 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 or 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. An adjustment is made for the deprecated binary formats in which eight bytes of binary header are used for the compression type. In this case, the eight bytes used for the compression type are 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-BASE8', 'X-BASE10' or 'X-BASE16', the data are 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 '<' or '>' 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 hexadecimal, 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 six-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 four bits of the second octet [(c1 & 3)<<4 | (c2>>4)], then the bottom four 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. X-BASE32K encoding is similar to BASE64 encoding, except that sets of 15 octets are encoded as sets of 8 16-bit unicode characters, by breaking the 120 bits into 8 15-bit quantities. 256 is added to each 15 bit quantity to bring it into a printable uncode range. When encoding, zero padding is used to fill out the last 15 bit quantity. If 8 or more bits of padding are used, a single equals sign (hexadecimal 003D) is appended. Embedded whitespace and newlines are introduced to produce lines of no more than 80 characters each. On decoding, all printable ascii characters and ascii whitespace characters are ignored except for any trailing equals signs. The number of trailing equals signs indicated the number of trailing octets to be trimmed from the end of the decoded data. (see Georgi Darakev, Vassil Litchev, Kostadin Z. Mitev, Herbert J. Bernstein, 'Efficient Support of Binary Data in the XML Implementation of the NeXus File Format',absract W0165, ACA Summer Meeting, Honolulu, HI, July 2006). 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 ARRAY_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 ARRAY_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. The detector may have a complex relationship between the raw intensity values and the number of incident photons. In most cases, the number stored in the final array will have a simple linear relationship to the actual number of incident photons, given by _array_intensities.gain. If raw, uncorrected values are presented (e.g. for calibration experiments), the value of _array_intensities.linearity will be 'raw' and _array_intensities.gain will not be used. ; _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 _array_intensities.pixel_fast_bin_size _array_intensities.pixel_slow_bin_size _array_intensities.pixel_binning_method image_1 linear 1.2 655535 0 2 2 hardware ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__array_intensities.array_id _item_description.description ; This item is a pointer to _array_structure.id in the ARRAY_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_DATA 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 count values should be divided to produce true photon 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 _item_units.code 'counts_per_photon' 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_range.maximum _item_range.minimum . 0.0 _item_units.code 'counts_per_photon' 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 method used to convert from the raw intensity to the stored element value: 'linear' is linear. '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 base 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. 'raw' means that the data are a set of raw values straight from the detector. ; _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 base 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. ; 'raw' ; The array consists of raw values to which no corrections have been applied. While the handling of the data is similar to that given for 'linear' data with no offset, the meaning of the data differs in that the number of incident photons is not necessarily linearly related to the number of counts reported. This value is intended for use either in calibration experiments or to allow for handling more complex data-fitting algorithms than are allowed for by this data item. ; save_ save__array_intensities.offset _item_description.description ; Offset value to add to array element values in the manner described by the 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.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 _item_units.code 'counts' save_ save__array_intensities.pixel_fast_bin_size _item_description.description ; The value of _array_intensities.pixel_fast_bin_size specifies the number of pixels that compose one element in the direction of the most rapidly varying array dimension. Typical values are 1, 2, 4 or 8. When there is 1 pixel per array element in both directions, the value given for _array_intensities.pixel_binning_method normally should be 'none'. It is specified as a float to allow for binning algorithms that create array elements that are not integer multiples of the detector pixel size. ; _item.name '_array_intensities.pixel_fast_bin_size' _item.category_id array_intensities _item.mandatory_code implicit _item_type.code float _item_default.value 1. loop_ _item_range.maximum _item_range.minimum . 0.0 _item_units.code 'pixels_per_element' save_ save__array_intensities.pixel_slow_bin_size _item_description.description ; The value of _array_intensities.pixel_slow_bin_size specifies the number of pixels that compose one element in the direction of the second most rapidly varying array dimension. Typical values are 1, 2, 4 or 8. When there is 1 pixel per array element in both directions, the value given for _array_intensities.pixel_binning_method normally should be 'none'. It is specified as a float to allow for binning algorithms that create array elements that are not integer multiples of the detector pixel size. ; _item.name '_array_intensities.pixel_slow_bin_size' _item.category_id array_intensities _item.mandatory_code implicit _item_type.code float _item_default.value 1. loop_ _item_range.maximum _item_range.minimum . 0.0 _item_units.code 'pixels_per_element' save_ save__array_intensities.pixel_binning_method _item_description.description ; The value of _array_intensities.pixel_binning_method specifies the method used to derive array elements from multiple pixels. ; _item.name '_array_intensities.pixel_binning_method' _item.category_id array_intensities _item.mandatory_code implicit _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail 'hardware' ; The element intensities were derived from the raw data of one or more pixels by used of hardware in the detector, e.g. by use of shift registers in a CCD to combine pixels into super-pixels. ; 'software' ; The element intensities were derived from the raw data of more than one pixel by use of software. ; 'combined' ; The element intensities were derived from the raw data of more than one pixel by use of both hardware and software, as when hardware binning is used in one direction and software in the other. ; 'none' ; In the both directions, the data has not been binned. The number of pixels is equal to the number of elements. When the value of _array_intensities.pixel_binning_method is 'none' the values of _array_intensities.pixel_fast_bin_size and _array_intensities.pixel_slow_bin_size both must be 1. ; 'unspecified' ; The method used to derive element intensities is not specified. ; _item_default.value 'unspecified' 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.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 that 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 VAXs 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. ; 'packed' ; Using the 'packed' compression scheme, a CCP4-style packing (International Tables for Crystallography Volume G, Section 5.6.3.2) ; 'canonical' ; Using the 'canonical' compression scheme (International Tables for Crystallography Volume G, Section 5.6.3.1) ; 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 754-1985 (IEEE, 1985). Ref: IEEE (1985). IEEE Standard for Binary Floating-Point Arithmetic. ANSI/IEEE Std 754-1985. New York: Institute of Electrical and Electronics Engineers. ; _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_data_frame.array_id' diffrn_data_frame 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_data_frame.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. The relationship to physical axes may be given. ; _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 the 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 _array_structure_list.axis_set_id image_1 1 1300 1 increasing ELEMENT_X image_1 2 1200 2 decreasing ELEMENY_Y ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__array_structure_list.array_id _item_description.description ; This item is a pointer to _array_structure.id in the ARRAY_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.axis_set_id _item_description.description ; This is a descriptor for the physical axis or set of axes corresponding to an array index. This data item is related to the axes of the detector itself given in DIFFRN_DETECTOR_AXIS, but usually differs in that the axes in this category are the axes of the coordinate system of reported data points, while the axes in DIFFRN_DETECTOR_AXIS are the physical axes of the detector describing the 'poise' of the detector as an overall physical object. If there is only one axis in the set, the identifier of that axis should be used as the identifier of the set. ; loop_ _item.name _item.category_id _item.mandatory_code '_array_structure_list.axis_set_id' array_structure_list yes '_array_structure_list_axis.axis_set_id' array_structure_list_axis implicit _item_type.code code loop_ _item_linked.child_name _item_linked.parent_name '_array_structure_list_axis.axis_set_id' '_array_structure_list.axis_set_id' 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 code 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_ ############################# # ARRAY_STRUCTURE_LIST_AXIS # ############################# save_ARRAY_STRUCTURE_LIST_AXIS _category.description ; Data items in the ARRAY_STRUCTURE_LIST_AXIS category describe the physical settings of sets of axes for the centres of pixels that correspond to data points described in the ARRAY_STRUCTURE_LIST category. In the simplest cases, the physical increments of a single axis correspond to the increments of a single array index. More complex organizations, e.g. spiral scans, may require coupled motions along multiple axes. Note that a spiral scan uses two coupled axes: one for the angular direction and one for the radial direction. This differs from a cylindrical scan for which the two axes are not coupled into one set. ; _category.id array_structure_list_axis _category.mandatory_code no loop_ _category_key.name '_array_structure_list_axis.axis_set_id' '_array_structure_list_axis.axis_id' loop_ _category_group.id 'inclusive_group' 'array_data_group' save_ save__array_structure_list_axis.axis_id _item_description.description ; The value of this data item is the identifier of one of the axes in the set of axes for which settings are being specified. Multiple axes may be specified for the same value of _array_structure_list_axis.axis_set_id. This item is a pointer to _axis.id in the AXIS category. ; _item.name '_array_structure_list_axis.axis_id' _item.category_id array_structure_list_axis _item.mandatory_code yes _item_type.code code save_ save__array_structure_list_axis.axis_set_id _item_description.description ; The value of this data item is the identifier of the set of axes for which axis settings are being specified. Multiple axes may be specified for the same value of _array_structure_list_axis.axis_set_id. This item is a pointer to _array_structure_list.axis_set_id in the ARRAY_STRUCTURE_LIST category. If this item is not specified, it defaults to the corresponding axis identifier. ; _item.name '_array_structure_list_axis.axis_set_id' _item.category_id array_structure_list_axis _item.mandatory_code implicit _item_type.code code save_ save__array_structure_list_axis.angle _item_description.description ; The setting of the specified axis in degrees for the first data point of the array index with the corresponding value of _array_structure_list.axis_set_id. If the index is specified as 'increasing', this will be the centre of the pixel with index value 1. If the index is specified as 'decreasing', this will be the centre of the pixel with maximum index value. ; _item.name '_array_structure_list_axis.angle' _item.category_id array_structure_list_axis _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'degrees' save_ save__array_structure_list_axis.angle_increment _item_description.description ; The pixel-centre-to-pixel-centre increment in the angular setting of the specified axis in degrees. This is not meaningful in the case of 'constant velocity' spiral scans and should not be specified for this case. See _array_structure_list_axis.angular_pitch. ; _item.name '_array_structure_list_axis.angle_increment' _item.category_id array_structure_list_axis _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'degrees' save_ save__array_structure_list_axis.displacement _item_description.description ; The setting of the specified axis in millimetres for the first data point of the array index with the corresponding value of _array_structure_list.axis_set_id. If the index is specified as 'increasing', this will be the centre of the pixel with index value 1. If the index is specified as 'decreasing', this will be the centre of the pixel with maximum index value. ; _item.name '_array_structure_list_axis.displacement' _item.category_id array_structure_list_axis _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'millimetres' save_ save__array_structure_list_axis.displacement_increment _item_description.description ; The pixel-centre-to-pixel-centre increment for the displacement setting of the specified axis in millimetres. ; _item.name '_array_structure_list_axis.displacement_increment' _item.category_id array_structure_list_axis _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'millimetres' save_ save__array_structure_list_axis.angular_pitch _item_description.description ; The pixel-centre-to-pixel-centre distance for a one-step change in the setting of the specified axis in millimetres. This is meaningful only for 'constant velocity' spiral scans or for uncoupled angular scans at a constant radius (cylindrical scans) and should not be specified for cases in which the angle between pixels (rather than the distance between pixels) is uniform. See _array_structure_list_axis.angle_increment. ; _item.name '_array_structure_list_axis.angular_pitch' _item.category_id array_structure_list_axis _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'millimetres' save_ save__array_structure_list_axis.radial_pitch _item_description.description ; The radial distance from one 'cylinder' of pixels to the next in millimetres. If the scan is a 'constant velocity' scan with differing angular displacements between pixels, the value of this item may differ significantly from the value of _array_structure_list_axis.displacement_increment. ; _item.name '_array_structure_list_axis.radial_pitch' _item.category_id array_structure_list_axis _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'millimetres' 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. Note: This choice of coordinate system is similar to but significantly different from the choice in MOSFLM (Leslie & Powell, 2004). In MOSFLM, X is along the X-ray beam (the CBF/imgCIF Z axis) and Z is along the rotation axis. 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 centre. The location of the beam centre on the detector should be given in the DIFFRN_DETECTOR category in distortion-corrected millimetres 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, it is necessary to specify the location of the beam centre on the detector in terms of the origin of the detector, which is, of course, not coincident with the centre of the sample. Ref: Leslie, A. G. W. & Powell, H. (2004). MOSFLM v6.11. MRC Laboratory of Molecular Biology, Hills Road, Cambridge, England. http://www.CCP4.ac.uk/dist/x-windows/Mosflm/. ; _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 Stout, G. H. & Jensen, L. H. (1989). X-ray structure determination. A practical guide, 2nd ed. p. 134. New York: Wiley Interscience]. 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. The order has been changed as a reminder that the ordering of presentation of tokens is not significant. The centre of rotation of the detector has been taken 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.depends_on 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.equipment 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 three-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 three-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 three-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 the category key for AXIS also includes the equipment. ; loop_ _item.name _item.category_id _item.mandatory_code '_axis.id' axis yes '_array_structure_list_axis.axis_id' array_structure_list_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' '_array_structure_list_axis.axis_id' '_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' or '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 three-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 three-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 three-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_ ##################### # DIFFRN_DATA_FRAME # ##################### save_DIFFRN_DATA_FRAME _category.description ; Data items in the DIFFRN_DATA_FRAME category record the details about each frame of data. The items in this category were previously in a DIFFRN_FRAME_DATA category, which is now deprecated. The items from the old category are provided as aliases but should not be used for new work. ; _category.id diffrn_data_frame _category.mandatory_code no loop_ _category_key.name '_diffrn_data_frame.id' '_diffrn_data_frame.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 are stored in four groups of binary data in the ARRAY_DATA category, linked by the array_id and binary_id. ; ; loop_ _diffrn_data_frame.id _diffrn_data_frame.detector_element_id _diffrn_data_frame.array_id _diffrn_data_frame.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_data_frame.array_id _item_description.description ; This item is a pointer to _array_structure.id in the ARRAY_STRUCTURE category. ; _item.name '_diffrn_data_frame.array_id' _item.category_id diffrn_data_frame _item.mandatory_code yes _item_aliases.alias_name '_diffrn_frame_data.array_id' _item_aliases.dictionary cif_img.dic _item_aliases.version 1.0 _item_type.code code save_ save__diffrn_data_frame.binary_id _item_description.description ; This item is a pointer to _array_data.binary_id in the ARRAY_DATA category. ; _item.name '_diffrn_data_frame.binary_id' _item.category_id diffrn_data_frame _item.mandatory_code implicit _item_aliases.alias_name '_diffrn_frame_data.binary_id' _item_aliases.dictionary cif_img.dic _item_aliases.version 1.0 _item_type.code int save_ save__diffrn_data_frame.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_data_frame.detector_element_id' _item.category_id diffrn_data_frame _item.mandatory_code yes _item_aliases.alias_name '_diffrn_frame_data.detector_element_id' _item_aliases.dictionary cif_img.dic _item_aliases.version 1.0 _item_type.code code save_ save__diffrn_data_frame.id _item_description.description ; The value of _diffrn_data_frame.id must uniquely identify each complete frame of data. ; loop_ _item.name _item.category_id _item.mandatory_code '_diffrn_data_frame.id' diffrn_data_frame 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_aliases.alias_name '_diffrn_frame_data.id' _item_aliases.dictionary cif_img.dic _item_aliases.version 1.0 _item_type.code code loop_ _item_linked.child_name _item_linked.parent_name '_diffrn_refln.frame_id' '_diffrn_data_frame.id' '_diffrn_scan.frame_id_start' '_diffrn_data_frame.id' '_diffrn_scan.frame_id_end' '_diffrn_data_frame.id' '_diffrn_scan_frame.frame_id' '_diffrn_data_frame.id' '_diffrn_scan_frame_axis.frame_id' '_diffrn_data_frame.id' save_ save__diffrn_data_frame.details _item_description.description ; The value of _diffrn_data_frame.details should give a description of special aspects of each frame of data. This is an appropriate location in which to record information from vendor headers as presented in those headers, but it should never be used as a substitute for providing the fully parsed information within the appropriate imgCIF/CBF categories. ; _item.name '_diffrn_data_frame.details' _item.category_id diffrn_data_frame _item.mandatory_code no _item_aliases.alias_name '_diffrn_frame_data.details' _item_aliases.dictionary cif_img.dic _item_aliases.version 1.4 _item_type.code text loop_ _item_examples.case _item_examples.detail ; HEADER_BYTES = 512; DIM = 2; BYTE_ORDER = big_endian; TYPE = unsigned_short; SIZE1 = 3072; SIZE2 = 3072; PIXEL_SIZE = 0.102588; BIN = 2x2; DETECTOR_SN = 901; TIME = 29.945155; DISTANCE = 200.000000; PHI = 85.000000; OSC_START = 85.000000; OSC_RANGE = 1.000000; WAVELENGTH = 0.979381; BEAM_CENTER_X = 157.500000; BEAM_CENTER_Y = 157.500000; PIXEL SIZE = 0.102588; OSCILLATION RANGE = 1; EXPOSURE TIME = 29.9452; TWO THETA = 0; BEAM CENTRE = 157.5 157.5; ; ; Example of header information extracted from an ADSC Quantum 315 detector header by CBFlib_0.7.6. Image provided by Chris Nielsen of ADSC from a data collection at SSRL beamline 1-5. ; save_ ########################################################################## # The following is a restatement of the mmCIF DIFFRN_DETECTOR, # # DIFFRN_MEASUREMENT and DIFFRN_RADIATION 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 'slow mode' 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 _item_type.code code save_ save__diffrn_detector.dtime _item_description.description ; The deadtime in microseconds of the detector(s) 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.detector_id' diffrn_detector_axis yes loop_ _item_linked.child_name _item_linked.parent_name '_diffrn_detector_axis.detector_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. Axes which are used to provide a coordinate system for the face of an area detetctor should not be counted for this data item. 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.detector_id' '_diffrn_detector_axis.axis_id' loop_ _category_group.id 'inclusive_group' 'diffrn_group' 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_ save__diffrn_detector_axis.detector_id _item_description.description ; This data item is a pointer to _diffrn_detector.id in the DIFFRN_DETECTOR category. This item was previously named _diffrn_detector_axis.id which is now a deprecated name. The old name is provided as an alias but should not be used for new work. ; _item.name '_diffrn_detector_axis.detector_id' _item.category_id diffrn_detector_axis _item.mandatory_code yes _item_aliases.alias_name '_diffrn_detector_axis.id' _item_aliases.dictionary cif_img.dic _item_aliases.version 1.0 _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. In most cases, giving more detailed information in ARRAY_STRUCTURE_LIST and ARRAY_STRUCTURE_LIST_AXIS is preferable to simply providing the centre of the detector element. ; _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 centre is slightly displaced from 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.detector_id _diffrn_detector_element.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 centre in millimetres from the (0, 0) (lower-left) corner of the detector element viewed from the sample side. The X and Y axes are the laboratory coordinate system coordinates defined in the AXIS category measured when all positioning axes for the detector are at their zero settings. If the resulting X or Y axis is then orthogonal to the detector, the Z axis is used instead of the orthogonal axis. ; _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 centre in millimetres from the (0, 0) (lower-left) corner of the detector element viewed from the sample side. The X and Y axes are the laboratory coordinate system coordinates defined in the AXIS category measured when all positioning axes for the detector are at their zero settings. If the resulting X or Y axis is then orthogonal to the detector, the Z axis is used instead of the orthogonal axis. ; _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_data_frame.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_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.device' '_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 ; 440 frames, 0.20 degrees, 150 sec, detector distance 12 cm, detector angle 22.5 degrees ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), 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. If the value of _diffrn_measurement.device is not given, it is implicitly equal to the value of _diffrn_measurement.diffrn_id. Either _diffrn_measurement.device or _diffrn_measurement.id may be used to link to other categories. If the experimental setup admits multiple devices, then _diffrn_measurement.id is used to provide a unique link. ; loop_ _item.name _item.category_id _item.mandatory_code '_diffrn_measurement.device' diffrn_measurement implicit '_diffrn_measurement_axis.measurement_device' diffrn_measurement_axis implicit loop_ _item_linked.child_name _item_linked.parent_name '_diffrn_measurement_axis.measurement_device' '_diffrn_measurement.device' _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' 'home-made' 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 _item_type.code code 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 the 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. Either _diffrn_measurement.device or _diffrn_measurement.id may be used to link to other categories. If the experimental setup admits multiple devices, then _diffrn_measurement.id is used to provide a unique link. ; loop_ _item.name _item.category_id _item.mandatory_code '_diffrn_measurement.id' diffrn_measurement implicit '_diffrn_measurement_axis.measurement_id' diffrn_measurement_axis implicit loop_ _item_linked.child_name _item_linked.parent_name '_diffrn_measurement_axis.measurement_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.measurement_device' '_diffrn_measurement_axis.measurement_id' '_diffrn_measurement_axis.axis_id' loop_ _category_group.id 'inclusive_group' 'diffrn_group' 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_ save__diffrn_measurement_axis.measurement_device _item_description.description ; This data item is a pointer to _diffrn_measurement.device in the DIFFRN_MEASUREMENT category. ; _item.name '_diffrn_measurement_axis.measurement_device' _item.category_id diffrn_measurement_axis _item.mandatory_code implicit _item_type.code text save_ save__diffrn_measurement_axis.measurement_id _item_description.description ; This data item is a pointer to _diffrn_measurement.id in the DIFFRN_MEASUREMENT category. This item was previously named _diffrn_measurement_axis.id, which is now a deprecated name. The old name is provided as an alias but should not be used for new work. ; _item.name '_diffrn_measurement_axis.measurement_id' _item.category_id diffrn_measurement_axis _item.mandatory_code implicit _item_aliases.alias_name '_diffrn_measurement_axis.id' _item_aliases.dictionary cif_img.dic _item_aliases.version 1.0 _item_type.code code save_ #################### # DIFFRN_RADIATION # #################### save_DIFFRN_RADIATION _category.description ; Data items in the DIFFRN_RADIATION category describe the radiation used for measuring diffraction intensities, its collimation and monochromatization before the sample. Post-sample treatment of the beam is described by data items in the DIFFRN_DETECTOR category. ; _category.id diffrn_radiation _category.mandatory_code no _category_key.name '_diffrn_radiation.diffrn_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_radiation.diffrn_id 'set1' _diffrn_radiation.collimation '0.3 mm double pinhole' _diffrn_radiation.monochromator 'graphite' _diffrn_radiation.type 'Cu K\a' _diffrn_radiation.wavelength_id 1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; ; _diffrn_radiation.wavelength_id 1 _diffrn_radiation.type 'Cu K\a' _diffrn_radiation.monochromator 'graphite' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__diffrn_radiation.collimation _item_description.description ; The collimation or focusing applied to the radiation. ; _item.name '_diffrn_radiation.collimation' _item.category_id diffrn_radiation _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_collimation' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case '0.3 mm double-pinhole' '0.5 mm' 'focusing mirrors' save_ save__diffrn_radiation.diffrn_id _item_description.description ; This data item is a pointer to _diffrn.id in the DIFFRN category. ; _item.name '_diffrn_radiation.diffrn_id' _item.mandatory_code yes _item_type.code code save_ save__diffrn_radiation.div_x_source _item_description.description ; Beam crossfire in degrees parallel to the laboratory X axis (see AXIS category). This is a characteristic of the X-ray beam as it illuminates the sample (or specimen) after all monochromation and collimation. This is the standard uncertainty (e.s.d.) of the directions of photons in the XZ plane around the mean source beam direction. Note that for some synchrotrons this value is specified in milliradians, in which case a conversion is needed. To convert a value in milliradians to a value in degrees, multiply by 0.180 and divide by \p. ; _item.name '_diffrn_radiation.div_x_source' _item.category_id diffrn_radiation _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__diffrn_radiation.div_y_source _item_description.description ; Beam crossfire in degrees parallel to the laboratory Y axis (see AXIS category). This is a characteristic of the X-ray beam as it illuminates the sample (or specimen) after all monochromation and collimation. This is the standard uncertainty (e.s.d.) of the directions of photons in the YZ plane around the mean source beam direction. Note that for some synchrotrons this value is specified in milliradians, in which case a conversion is needed. To convert a value in milliradians to a value in degrees, multiply by 0.180 and divide by \p. ; _item.name '_diffrn_radiation.div_y_source' _item.category_id diffrn_radiation _item.mandatory_code no _item_type.code float _item_units.code degrees _item_default.value 0.0 save_ save__diffrn_radiation.div_x_y_source _item_description.description ; Beam crossfire correlation degrees^2^ between the crossfire laboratory X-axis component and the crossfire laboratory Y-axis component (see AXIS category). This is a characteristic of the X-ray beam as it illuminates the sample (or specimen) after all monochromation and collimation. This is the mean of the products of the deviations of the direction of each photon in XZ plane times the deviations of the direction of the same photon in the YZ plane around the mean source beam direction. This will be zero for uncorrelated crossfire. Note that some synchrotrons, this value is specified in milliradians^2^, in which case a conversion would be needed. To go from a value in milliradians^2^ to a value in degrees^2^, multiply by 0.180^2^ and divide by \p^2^. ; _item.name '_diffrn_radiation.div_x_y_source' _item.category_id diffrn_radiation _item.mandatory_code no _item_type.code float _item_units.code degrees_squared _item_default.value 0.0 save_ save__diffrn_radiation.filter_edge _item_description.description ; Absorption edge in \%Angstroms of the radiation filter used. ; _item.name '_diffrn_radiation.filter_edge' _item.category_id diffrn_radiation _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_filter_edge' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__diffrn_radiation.inhomogeneity _item_description.description ; Half-width in millimetres of the incident beam in the direction perpendicular to the diffraction plane. ; _item.name '_diffrn_radiation.inhomogeneity' _item.category_id diffrn_radiation _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_inhomogeneity' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code millimetres save_ save__diffrn_radiation.monochromator _item_description.description ; The method used to obtain monochromatic radiation. If a monochromator crystal is used, the material and the indices of the Bragg reflection are specified. ; _item.name '_diffrn_radiation.monochromator' _item.category_id diffrn_radiation _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_monochromator' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case 'Zr filter' 'Ge 220' 'none' 'equatorial mounted graphite' save_ save__diffrn_radiation.polarisn_norm _item_description.description ; The angle in degrees, as viewed from the specimen, between the perpendicular component of the polarization and the diffraction plane. See _diffrn_radiation_polarisn_ratio. ; _item.name '_diffrn_radiation.polarisn_norm' _item.category_id diffrn_radiation _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_polarisn_norm' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 90.0 90.0 90.0 -90.0 -90.0 -90.0 _item_type.code float _item_units.code degrees save_ save__diffrn_radiation.polarisn_ratio _item_description.description ; Polarization ratio of the diffraction beam incident on the crystal. This is the ratio of the perpendicularly polarized to the parallel polarized component of the radiation. The perpendicular component forms an angle of _diffrn_radiation.polarisn_norm to the normal to the diffraction plane of the sample (i.e. the plane containing the incident and reflected beams). ; _item.name '_diffrn_radiation.polarisn_ratio' _item.category_id diffrn_radiation _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_polarisn_ratio' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__diffrn_radiation.polarizn_source_norm _item_description.description ; The angle in degrees, as viewed from the specimen, between the normal to the polarization plane and the laboratory Y axis as defined in the AXIS category. Note that this is the angle of polarization of the source photons, either directly from a synchrotron beamline or from a monochromater. This differs from the value of _diffrn_radiation.polarisn_norm in that _diffrn_radiation.polarisn_norm refers to polarization relative to the diffraction plane rather than to the laboratory axis system. In the case of an unpolarized beam, or a beam with true circular polarization, in which no single plane of polarization can be determined, the plane should be taken as the XZ plane and the angle as 0. See _diffrn_radiation.polarizn_source_ratio. ; _item.name '_diffrn_radiation.polarizn_source_norm' _item.category_id diffrn_radiation _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum 90.0 90.0 90.0 -90.0 -90.0 -90.0 _item_type.code float _item_units.code degrees _item_default.value 0.0 save_ save__diffrn_radiation.polarizn_source_ratio _item_description.description ; (Ip-In)/(Ip+In), where Ip is the intensity (amplitude squared) of the electric vector in the plane of polarization and In is the intensity (amplitude squared) of the electric vector in the plane of the normal to the plane of polarization. In the case of an unpolarized beam, or a beam with true circular polarization, in which no single plane of polarization can be determined, the plane is to be taken as the XZ plane and the normal is parallel to the Y axis. Thus, if there was complete polarization in the plane of polarization, the value of _diffrn_radiation.polarizn_source_ratio would be 1, and for an unpolarized beam _diffrn_radiation.polarizn_source_ratio would have a value of 0. If the X axis has been chosen to lie in the plane of polarization, this definition will agree with the definition of 'MONOCHROMATOR' in the Denzo glossary, and values of near 1 should be expected for a bending-magnet source. However, if the X axis were perpendicular to the polarization plane (not a common choice), then the Denzo value would be the negative of _diffrn_radiation.polarizn_source_ratio. See http://www.hkl-xray.com for information on Denzo and Otwinowski & Minor (1997). This differs both in the choice of ratio and choice of orientation from _diffrn_radiation.polarisn_ratio, which, unlike _diffrn_radiation.polarizn_source_ratio, is unbounded. Reference: Otwinowski, Z. & Minor, W. (1997). 'Processing of X-ray diffraction data collected in oscillation mode.' Methods Enzymol. 276, 307-326. ; _item.name '_diffrn_radiation.polarizn_source_ratio' _item.category_id diffrn_radiation _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum 1.0 1.0 1.0 -1.0 -1.0 -1.0 _item_type.code float save_ save__diffrn_radiation.probe _item_description.description ; Name of the type of radiation used. It is strongly recommended that this be given so that the probe radiation is clearly specified. ; _item.name '_diffrn_radiation.probe' _item.category_id diffrn_radiation _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_probe' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_enumeration.value 'x-ray' 'neutron' 'electron' 'gamma' save_ save__diffrn_radiation.type _item_description.description ; The nature of the radiation. This is typically a description of the X-ray wavelength in Siegbahn notation. ; _item.name '_diffrn_radiation.type' _item.category_id diffrn_radiation _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_type' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case 'CuK\a' 'Cu K\a~1~' 'Cu K-L~2,3~' 'white-beam' save_ save__diffrn_radiation.xray_symbol _item_description.description ; The IUPAC symbol for the X-ray wavelength for the probe radiation. ; _item.name '_diffrn_radiation.xray_symbol' _item.category_id diffrn_radiation _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_xray_symbol' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_enumeration.value _item_enumeration.detail 'K-L~3~' 'K\a~1~ in older Siegbahn notation' 'K-L~2~' 'K\a~2~ in older Siegbahn notation' 'K-M~3~' 'K\b~1~ in older Siegbahn notation' 'K-L~2,3~' 'use where K-L~3~ and K-L~2~ are not resolved' save_ save__diffrn_radiation.wavelength_id _item_description.description ; This data item is a pointer to _diffrn_radiation_wavelength.id in the DIFFRN_RADIATION_WAVELENGTH category. ; _item.name '_diffrn_radiation.wavelength_id' _item.category_id diffrn_radiation _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_data_frame.id in the DIFFRN_DATA_FRAME 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. In this example, three rotation axes and one translation axis at nonzero values are specified, with one axis stepping. There is no reason why more axes could not have been specified to step. Range information has been specified, but note that it can be calculated from the number of frames and the increment, so the data item _diffrn_scan_axis.angle_range could be dropped. Both the sweep data and the data for a single frame are specified. Note that the information on how the axes are stepped is given twice, once in terms of the overall averages in the value of _diffrn_scan.integration_time and the values for DIFFRN_SCAN_AXIS, and precisely for the given frame in the value for _diffrn_scan_frame.integration_time and the values for DIFFRN_SCAN_FRAME_AXIS. If dose-related adjustments are made to scan times and nonlinear stepping is done, these values may differ. Therefore, in interpreting the data for a particular frame it is important to use the frame-specific data. ; ; _diffrn_scan.id 1 _diffrn_scan.date_start '2001-11-18T03:26:42' _diffrn_scan.date_end '2001-11-18T03:36:45' _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.date '2001-11-18T03:27:33' _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.angle_increment _diffrn_scan_frame_axis.displacement _diffrn_scan_frame_axis.displacement_increment mad_L2_018 omega 201.8 0.1 . . mad_L2_018 kappa -40.0 0.0 . . mad_L2_018 phi 127.5 0.0 . . mad_L2_018 tranz . . 2.3 0.0 ; ; Example 2 - a more extensive example (R. M. Sweet, P. J. Ellis & H. J. Bernstein). A detector is placed 240 mm along the Z axis from the goniometer. This leads to a choice: either the axes of the detector are defined at the origin, and then a Z setting of -240 is entered, or the axes are defined with the necessary Z offset. In this case, the setting is used and the offset is left as zero. This axis is called DETECTOR_Z. The axis for positioning the detector in the Y direction depends on the detector Z axis. This axis is called DETECTOR_Y. The axis for positioning the detector in the X direction depends on the detector Y axis (and therefore on the detector Z axis). This axis is called DETECTOR_X. This detector may be rotated around the Y axis. This rotation axis depends on the three translation axes. It is called DETECTOR_PITCH. A coordinate system is defined on the face of the detector in terms of 2300 0.150 mm pixels in each direction. The ELEMENT_X axis is used to index the first array index of the data array and the ELEMENT_Y axis is used to index the second array index. Because the pixels are 0.150mm x 0.150mm, the centre of the first pixel is at (0.075, 0.075) in this coordinate system. ; ; ###CBF: VERSION 1.1 data_image_1 # category DIFFRN _diffrn.id P6MB _diffrn.crystal_id P6MB_CRYSTAL7 # category DIFFRN_SOURCE loop_ _diffrn_source.diffrn_id _diffrn_source.source _diffrn_source.type P6MB synchrotron 'SSRL beamline 9-1' # category DIFFRN_RADIATION loop_ _diffrn_radiation.diffrn_id _diffrn_radiation.wavelength_id _diffrn_radiation.monochromator _diffrn_radiation.polarizn_source_ratio _diffrn_radiation.polarizn_source_norm _diffrn_radiation.div_x_source _diffrn_radiation.div_y_source _diffrn_radiation.div_x_y_source P6MB WAVELENGTH1 'Si 111' 0.8 0.0 0.08 0.01 0.00 # category DIFFRN_RADIATION_WAVELENGTH loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt WAVELENGTH1 0.98 1.0 # category DIFFRN_DETECTOR loop_ _diffrn_detector.diffrn_id _diffrn_detector.id _diffrn_detector.type _diffrn_detector.number_of_axes P6MB MAR345-SN26 'MAR 345' 4 # category DIFFRN_DETECTOR_AXIS loop_ _diffrn_detector_axis.detector_id _diffrn_detector_axis.axis_id MAR345-SN26 DETECTOR_X MAR345-SN26 DETECTOR_Y MAR345-SN26 DETECTOR_Z MAR345-SN26 DETECTOR_PITCH # category DIFFRN_DETECTOR_ELEMENT loop_ _diffrn_detector_element.id _diffrn_detector_element.detector_id ELEMENT1 MAR345-SN26 # category DIFFRN_DATA_FRAME loop_ _diffrn_data_frame.id _diffrn_data_frame.detector_element_id _diffrn_data_frame.array_id _diffrn_data_frame.binary_id FRAME1 ELEMENT1 ARRAY1 1 # category DIFFRN_MEASUREMENT loop_ _diffrn_measurement.diffrn_id _diffrn_measurement.id _diffrn_measurement.number_of_axes _diffrn_measurement.method P6MB GONIOMETER 3 rotation # category DIFFRN_MEASUREMENT_AXIS loop_ _diffrn_measurement_axis.measurement_id _diffrn_measurement_axis.axis_id GONIOMETER GONIOMETER_PHI GONIOMETER GONIOMETER_KAPPA GONIOMETER GONIOMETER_OMEGA # category DIFFRN_SCAN loop_ _diffrn_scan.id _diffrn_scan.frame_id_start _diffrn_scan.frame_id_end _diffrn_scan.frames SCAN1 FRAME1 FRAME1 1 # category DIFFRN_SCAN_AXIS 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 SCAN1 GONIOMETER_OMEGA 12.0 1.0 1.0 0.0 0.0 0.0 SCAN1 GONIOMETER_KAPPA 23.3 0.0 0.0 0.0 0.0 0.0 SCAN1 GONIOMETER_PHI -165.8 0.0 0.0 0.0 0.0 0.0 SCAN1 DETECTOR_Z 0.0 0.0 0.0 -240.0 0.0 0.0 SCAN1 DETECTOR_Y 0.0 0.0 0.0 0.6 0.0 0.0 SCAN1 DETECTOR_X 0.0 0.0 0.0 -0.5 0.0 0.0 SCAN1 DETECTOR_PITCH 0.0 0.0 0.0 0.0 0.0 0.0 # category DIFFRN_SCAN_FRAME loop_ _diffrn_scan_frame.frame_id _diffrn_scan_frame.frame_number _diffrn_scan_frame.integration_time _diffrn_scan_frame.scan_id _diffrn_scan_frame.date FRAME1 1 20.0 SCAN1 1997-12-04T10:23:48 # category DIFFRN_SCAN_FRAME_AXIS loop_ _diffrn_scan_frame_axis.frame_id _diffrn_scan_frame_axis.axis_id _diffrn_scan_frame_axis.angle _diffrn_scan_fra