<HTML> <HEAD> <TITLE>cif_img.dic v1.2.3</TITLE> </HEAD> <body bgcolor="#FAFAFF" text="#0808A0" BACKGROUND="../html_graphics/cbflibbackground.jpg"> <font color="#0808A0"> <H1> # <a href="http://www.iucr.org/iucr-top/welcome.html"> <img alt="[IUCr Home Page]" src="../html_graphics/iucrhome.jpg" ALIGN=MIDDLE></a> <a href="http://www.iucr.org/iucr-top/cif/home.html"> <img alt="[CIF Home Page]" src="../html_graphics/cifhome.jpg" ALIGN=MIDDLE></a> <A HREF="cbf_definition_rev.html"><IMG SRC="../html_graphics/CBFbutton.jpg" ALT="[CBF/imgCIF]" ALIGN=MIDDLE></A> <A HREF="CBFlib.html"><IMG SRC="../html_graphics/cbflibbutton.jpg" ALT="[CBFlib]" ALIGN=MIDDLE></A> # </H1> <H1 ALIGN=CENTER> # <IMG SRC="../html_graphics/CBFbig.jpg" ALIGN=MIDDLE ALT="imgCIF/CBF"> # </H1> <H1 ALIGN=CENTER># Extensions Dictionary #</H2> </font><font color="#000000"> <PRE> ############################################################################## # # # Image CIF Dictionary (imgCIF) # # and Crystallographic Binary File Dictionary (CBF) # # Extending the Macromolecular CIF Dictionary (mmCIF) # # # # Version 1.2.3 # # of 2001-07-04 # # by Andrew P. Hammersley, Herbert J. Bernstein and John D. Westbrook # # # # This dictionary was adapted from the imgCIF Workshop, held at BNL Oct 1997# # and the Crystallographic Binary File Format Draft Proposal by Andy # # 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 and others. # ############################################################################## data_cif_img.dic _dictionary.title cif_img.dic _dictionary.version 1.2.3 _dictionary.datablock_id cif_img.dic ############################################################################## # CONTENTS # # <a href="#CATEGORY_GROUP_LIST">CATEGORY_GROUP_LIST</a> # # category <a href="#ARRAY_DATA">ARRAY_DATA</a> # # <a href="#_array_data.array_id" >_array_data.array_id</a> # <a href="#_array_data.binary_id" >_array_data.binary_id</a> # <a href="#_array_data.data" >_array_data.data</a> # # category <a href="#ARRAY_ELEMENT_SIZE">ARRAY_ELEMENT_SIZE</a> # # <a href="#_array_element_size.array_id" >_array_element_size.array_id</a> # <a href="#_array_element_size.index" >_array_element_size.index</a> # <a href="#_array_element_size.size" >_array_element_size.size</a> # # category <a href="#ARRAY_INTENSITIES">ARRAY_INTENSITIES</a> # # <a href="#_array_intensities.array_id" >_array_intensities.array_id</a> # <a href="#_array_intensities.binary_id" >_array_intensities.binary_id</a> # <a href="#_array_intensities.gain" >_array_intensities.gain</a> # <a href="#_array_intensities.gain_esd" >_array_intensities.gain_esd</a> # <a href="#_array_intensities.linearity" >_array_intensities.linearity</a> # <a href="#_array_intensities.offset" >_array_intensities.offset</a> # <a href="#_array_intensities.scaling" >_array_intensities.scaling</a> # <a href="#_array_intensities.overload" >_array_intensities.overload</a> # <a href="#_array_intensities.undefined_value" >_array_intensities.undefined_value</a> # # category <a href="#ARRAY_STRUCTURE">ARRAY_STRUCTURE</a> # # <a href="#_array_structure.byte_order" >_array_structure.byte_order</a> # <a href="#_array_structure.compression_type" >_array_structure.compression_type</a> # <a href="#_array_structure.encoding_type" >_array_structure.encoding_type</a> # <a href="#_array_structure.id" >_array_structure.id</a> # # category <a href="#ARRAY_STRUCTURE_LIST">ARRAY_STRUCTURE_LIST</a> # # <a href="#_array_structure_list.axis_set_id" >_array_structure_list.axis_set_id</a> # <a href="#_array_structure_list.array_id" >_array_structure_list.array_id</a> # <a href="#_array_structure_list.dimension" >_array_structure_list.dimension</a> # <a href="#_array_structure_list.direction" >_array_structure_list.direction</a> # <a href="#_array_structure_list.index" >_array_structure_list.index</a> # <a href="#_array_structure_list.precedence" >_array_structure_list.precedence</a> # # category <a href="#ARRAY_STRUCTURE_LIST_AXIS">ARRAY_STRUCTURE_LIST_AXIS</a> # # <a href="#_array_structure_list_axis.axis_id" >_array_structure_list_axis.axis_id</a> # <a href="#_array_structure_list_axis.axis_set_id" >_array_structure_list_axis.axis_set_id</a> # <a href="#_array_structure_list_axis.angle" >_array_structure_list_axis.angle</a> # <a href="#_array_structure_list_axis.angle_increment" >_array_structure_list_axis.angle_increment</a> # <a href="#_array_structure_list_axis.displacement" >_array_structure_list_axis.displacement_increment</a> # <a href="#_array_structure_list_axis.angular_pitch" >_array_structure_list_axis.angular_pitch</a> # <a href="#_array_structure_list_axis.radial_pitch" >_array_structure_list_axis.radial_pitch</a> # # category <a href="#AXIS">AXIS</a> # # <a href="#_axis.depends_on" >_axis.depends_on</a> # <a href="#_axis.equipment" >_axis.equipment</a> # <a href="#_axis.id" >_axis.id</a></a> # <a href="#_axis.offset[1]" >_axis.offset[1]</a> # <a href="#_axis.offset[2]" >_axis.offset[2]</a> # <a href="#_axis.offset[3]" >_axis.offset[3]</a> # <a href="#_axis.type" >_axis.type</a> # <a href="#_axis.vector[1]" >_axis.vector[1]</a> # <a href="#_axis.vector[2]" >_axis.vector[2]</a> # <a href="#_axis.vector[3]" >_axis.vector[3]</a> # # category <a href="#DIFFRN_DATA_FRAME">DIFFRN_DATA_FRAME</a> # # <a href="#_diffrn_data_frame.array_id" >_diffrn_data_frame.array_id</a> # <a href="#_diffrn_data_frame.binary_id" >_diffrn_data_frame.binary_id</a> # <a href="#_diffrn_data_frame.detector_element_id" >_diffrn_data_frame.detector_element_id</a> # <a href="#_diffrn_data_frame.id" >_diffrn_data_frame.id</a> # # category <a href="#DIFFRN_DETECTOR">DIFFRN_DETECTOR</a> # # <a href="#_diffrn_detector.details" >_diffrn_detector.details</a> # <a href="#_diffrn_detector.detector" >_diffrn_detector.detector</a> # <a href="#_diffrn_detector.diffrn_id" >_diffrn_detector.diffrn_id</a> # <a href="#_diffrn_detector.dtime" >_diffrn_detector.dtime</a> # <a href="#_diffrn_detector.id" >_diffrn_detector.id</a> # <a href="#_diffrn_detector.number_of_axes" >_diffrn_detector.number_of_axes</a> # <a href="#_diffrn_detector.type" >_diffrn_detector.type</a> # # category <a href="#DIFFRN_DETECTOR_AXIS">DIFFRN_DETECTOR_AXIS</a> # # <a href="#_diffrn_detector_axis.axis_id" >_diffrn_detector_axis.axis_id</a> # <a href="#_diffrn_detector_axis.detector_id" >_diffrn_detector_axis.detector_id</a> # # category <a href="#DIFFRN_DETECTOR_ELEMENT">DIFFRN_DETECTOR_ELEMENT</a> # # <a href="#_diffrn_detector_element.center[1]" >_diffrn_detector_element.center[1]</a> # <a href="#_diffrn_detector_element.center[2]" >_diffrn_detector_element.center[2]</a> # <a href="#_diffrn_detector_element.id" >_diffrn_detector_element.id</a> # <a href="#_diffrn_detector_element.detector_id" >_diffrn_detector_element.detector_id</a> # # category <a href="#DIFFRN_MEASUREMENT">DIFFRN_MEASUREMENT</a> # # <a href="#_diffrn_measurement.diffrn_id" >_diffrn_measurement.diffrn_id</a> # <a href="#_diffrn_measurement.details" >_diffrn_measurement.details</a> # <a href="#_diffrn_measurement.device" >_diffrn_measurement.device</a> # <a href="#_diffrn_measurement.device_details" >_diffrn_measurement.device_details</a> # <a href="#_diffrn_measurement.device_type" >_diffrn_measurement.device_type</a> # <a href="#_diffrn_measurement.id" >_diffrn_measurement.id</a> # <a href="#_diffrn_measurement.method" >_diffrn_measurement.method</a> # <a href="#_diffrn_measurement.number_of_axes" >_diffrn_measurement.number_of_axes</a> # <a href="#_diffrn_measurement.specimen_support" >_diffrn_measurement.specimen_support</a> # # category <a href="#DIFFRN_MEASUREMENT_AXIS">DIFFRN_MEASUREMENT_AXIS</a> # # <a href="#_diffrn_measurement_axis.id" >_diffrn_measurement_axis.axis_id</a> # <a href="#_diffrn_measurement_axis.measurement_device" >_diffrn_measurement_axis.measurement_device</a> # <a href="#_diffrn_measurement_axis.measurement_id" >_diffrn_measurement_axis.measurement_id</a> # # category <a href="#DIFFRN_RADIATION">DIFFRN_RADIATION</a> # # <A HREF="#_diffrn_radiation.collimation">_diffrn_radiation.collimation</A> # <A HREF="#_diffrn_radiation.diffrn_id">_diffrn_radiation.diffrn_id</A> # <a href="#_diffrn_radiation.div_x_source" >_diffrn_radiation.div_x_source</a> # <a href="#_diffrn_radiation.div_y_source" >_diffrn_radiation.div_y_source</a> # <a href="#_diffrn_radiation.div_x_y_source" >_diffrn_radiation.div_x_y_source</a> # <A HREF="#_diffrn_radiation.filter_edge">_diffrn_radiation.filter_edge</A>' # <A HREF="#_diffrn_radiation.inhomogeneity">_diffrn_radiation.inhomogeneity</A> # <A HREF="#_diffrn_radiation.monochromator">_diffrn_radiation.monochromator</A> # <A HREF="#_diffrn_radiation.polarisn_norm">_diffrn_radiation.polarisn_norm</A> # <A HREF="#_diffrn_radiation.polarisn_ratio">_diffrn_radiation.polarisn_ratio</A> # <a href="#_diffrn_radiation.polarizn_source_norm" >_diffrn_radiation.polarizn_source_norm</a> # <a href="#_diffrn_radiation.polarizn_source_ratio" >_diffrn_radiation.polarizn_source_ratio</a> # <A HREF="#_diffrn_radiation.probe">_diffrn_radiation.probe</A> # <A HREF="#_diffrn_radiation.type">_diffrn_radiation.type</A> # <A HREF="#_diffrn_radiation.xray_symbol">_diffrn_radiation.xray_symbol</A> # <A HREF="#_diffrn_radiation.wavelength_id">_diffrn_radiation.wavelength_id</A> # # category <a href="#DIFFRN_REFLN">DIFFRN_REFLN</a> # # <a href="#_diffrn_refln.frame_id" >_diffrn_refln.frame_id</a> # # category <a href="#DIFFRN_SCAN">DIFFRN_SCAN</a> # # <a href="#_diffrn_scan.id" >_diffrn_scan.id</a> # <a href="#_diffrn_scan.date_end" >_diffrn_scan.date_end</a> # <a href="#_diffrn_scan.date_start" >_diffrn_scan.date_start</a> # <a href="#_diffrn_scan.integration_time" >_diffrn_scan.integration_time</a> # <a href="#_diffrn_scan.frame_id_start" >_diffrn_scan.frame_id_start</a> # <a href="#_diffrn_scan.frame_id_end" >_diffrn_scan.frame_id_end</a> # <a href="#_diffrn_scan.frames" >_diffrn_scan.frames</a> # # category <a href="#DIFFRN_SCAN_AXIS">DIFFRN_SCAN_AXIS</a> # # <a href="#_diffrn_scan_axis.axis_id" >_diffrn_scan_axis.axis_id</a> # <a href="#_diffrn_scan_axis.angle_start" >_diffrn_scan_axis.angle_start</a> # <a href="#_diffrn_scan_axis.angle_range" >_diffrn_scan_axis.angle_range</a> # <a href="#_diffrn_scan_axis.angle_increment" >_diffrn_scan_axis.angle_increment</a> # <a href="#_diffrn_scan_axis.angle_rstrt_incr" >_diffrn_scan_axis.angle_rstrt_incr</a> # <a href="#_diffrn_scan_axis.displacement_start" >_diffrn_scan_axis.displacement_start</a> # <a href="#_diffrn_scan_axis.displacement_range" >_diffrn_scan_axis.displacement_range</a> # <a href="#_diffrn_scan_axis.displacement_increment" >_diffrn_scan_axis.displacement_increment</a> # <a href="#_diffrn_scan_axis.displacement_rstrt_incr" >_diffrn_scan_axis.displacement_rstrt_incr</a> # <a href="#_diffrn_scan_axis.scan_id" >_diffrn_scan_axis.scan_id</a> # # category <a href="#DIFFRN_SCAN_FRAME">DIFFRN_SCAN_FRAME</a> # # <a href="#_diffrn_scan_frame.date" >_diffrn_scan_frame.date</a> # <a href="#_diffrn_scan_frame.frame_id" >_diffrn_scan_frame.frame_id</a> # <a href="#_diffrn_scan_frame.frame_number" >_diffrn_scan_frame.frame_number</a> # <a href="#_diffrn_scan_frame.integration_time" >_diffrn_scan_frame.integration_time</a> # <a href="#_diffrn_scan_frame.scan_id" >_diffrn_scan_frame.scan_id</a> # # category <a href="#DIFFRN_SCAN_FRAME_AXIS">DIFFRN_SCAN_FRAME_AXIS</a> # # <a href="#_diffrn_scan_frame_axis.axis_id" >_diffrn_scan_frame_axis.axis_id</a> # <a href="#_diffrn_scan_frame_axis.angle" >_diffrn_scan_frame_axis.angle</a> # <a href="#_diffrn_scan_frame_axis.angle_increment" >_diffrn_scan_frame_axis.angle_increment</a> # <a href="#_diffrn_scan_frame_axis.angle_rstrt_incr" >_diffrn_scan_frame_axis.angle_rstrt_incr</a> # <a href="#_diffrn_scan_frame_axis.displacement" >_diffrn_scan_frame_axis.displacement</a> # <a href="#_diffrn_scan_frame_axis.displacement_increment" >_diffrn_scan_frame_axis.displacement_increment</a> # <a href="#_diffrn_scan_frame_axis.displacement_rstrt_incr" >_diffrn_scan_frame_axis.displacement_rstrt_incr</a> # <a href="#_diffrn_scan_frame_axis.frame_id" >_diffrn_scan_frame_axis.frame_id</a> # # <a href="#ITEM_TYPE_LIST">ITEM_TYPE_LIST</a> # <a href="#ITEM_UNITS_LIST">ITEM_UNITS_LIST</a> # <a href="#DICTIONARY_HISTORY">DICTIONARY_HISTORY</a> # ############################################################################## ######################### ## <a name="CATEGORY_GROUP_LIST">CATEGORY_GROUP_LIST</a> ## ######################### 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. ; ############## # <a name="ARRAY_DATA">ARRAY_DATA</a> # ############## save_ARRAY_DATA _category.description ; Data items in the <a href="#ARRAY_DATA">ARRAY_DATA</a> category are the containers for the array data items described in category <a href="#ARRAY_STRUCTURE">ARRAY_STRUCTURE</a>. ; _category.id array_data _category.mandatory_code no loop_ _category_key.name '<a href="#_array_data.array_id" >_array_data.array_id</a>' '<a href="#_array_data.binary_id" >_array_data.binary_id</a>' loop_ _category_group.id 'inclusive_group' 'array_data_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - This example shows two binary data blocks. The first one was compressed by the CBF_CANONICAL compression algorithm and presented as hexadecimal data. The first character "H" on the data lines means hexadecimal. It could have been "O" for octal or "D" for decimal. The second character on the line shows the number of bytes in each word (in this case "4"), which then requires 8 hexadecimal digits per word. The third character gives the order of octets within a word, in this case "<" for the ordering 4321 (i.e. "big-endian"). Alternatively the character ">" could have been used for the ordering 1234 (i.e. "little-endian"). The block has a "message digest" to check the integrity of the data. The second block is similar, but uses CBF_PACKED compression and BASE64 encoding. Note that the size and the digest are different. ; ; loop_ <a href="#_array_data.array_id" >_array_data.array_id</a> <a href="#_array_data.binary_id" >_array_data.binary_id</a> <a href="#_array_data.data" >_array_data.data</a> image_1 1 ; --CIF-BINARY-FORMAT-SECTION-- Content-Type: application/octet-stream; conversions="x-CBF_CANONICAL" Content-Transfer-Encoding: X-BASE16 X-Binary-Size: 3927126 X-Binary-ID: 1 Content-MD5: u2sTJEovAHkmkDjPi+gWsg== # Hexadecimal encoding, byte 0, byte order ...21 # H4< 0050B810 00000000 00000000 00000000 000F423F 00000000 00000000 ... .... --CIF-BINARY-FORMAT-SECTION---- ; image_2 2 ; --CIF-BINARY-FORMAT-SECTION-- Content-Type: application/octet-stream; conversions="x-CBF-PACKED" Content-Transfer-Encoding: BASE64 X-Binary-Size: 3745758 X-Binary-ID: 1 Content-MD5: 1zsJjWPfol2GYl2V+QSXrw== ELhQAAAAAAAA... ... --CIF-BINARY-FORMAT-SECTION---- ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save_<a name="_array_data.array_id" >_array_data.array_id</a> _item_description.description ; This item is a pointer to <a href="#_array_structure.id" >_array_structure.id</a> in the <a href="#ARRAY_STRUCTURE">ARRAY_STRUCTURE</a> category. ; _item.name '<a href="#_array_data.array_id" >_array_data.array_id</a>' _item.category_id array_data _item.mandatory_code yes _item_type.code code save_ save_<a name="_array_data.binary_id" >_array_data.binary_id</a> _item_description.description ; This item is an integer identifier which, along with <a href="#_array_data.array_id" >_array_data.array_id</a> should uniquely identify the particular block of array data. If <a href="#_array_data.binary_id" >_array_data.binary_id</a> is not explicitly given, it defaults to 1. The value of <a href="#_array_data.binary_id" >_array_data.binary_id</a> distinguishes among multiple sets of data with the same array structure. If the MIME header of the data array specifies a value for X-Binary-Id, these values should be equal. ; loop_ _item.name _item.category_id _item.mandatory_code '<a href="#_array_data.binary_id" >_array_data.binary_id</a>' array_data implicit '<a href="#_diffrn_data_frame.binary_id" >_diffrn_data_frame.binary_id</a>' diffrn_data_frame implicit '<a href="#_array_intensities.binary_id" >_array_intensities.binary_id</a>' array_intensities implicit loop_ _item_linked.child_name _item_linked.parent_name '<a href="#_diffrn_data_frame.binary_id" >_diffrn_data_frame.binary_id</a>' '<a href="#_array_data.binary_id" >_array_data.binary_id</a>' '<a href="#_array_intensities.binary_id" >_array_intensities.binary_id</a>' '<a href="#_array_data.binary_id" >_array_data.binary_id</a>' _item_default.value 1 _item_type.code int loop_ _item_range.maximum _item_range.minimum 1 1 . 1 save_ save_<a name="_array_data.data" >_array_data.data</a> _item_description.description ; The value of <a href="#_array_data.data" >_array_data.data</a> contains the array data encapsulated in a STAR string. The representation used is a variant on the Multipurpose Internet Mail Extensions (MIME) specified in RFC 2045-2049 by N. Freed et al. The boundary delimiter used in writing an imgCIF or CBF is "--CIF-BINARY-FORMAT-SECTION--" (including the required initial "--"). The Content-Type may be any of the discrete types permitted in RFC 2045; "application/octet-stream" is recommended. If an octet stream was compressed, the compression should be specified by the parameter 'conversions="x-CBF_PACKED"' or the parameter 'conversions="x-CBF_CANONICAL"'. The Content-Transfer-Encoding may be "BASE64", "Quoted-Printable", "X-BASE8", "X-BASE10", or "X-BASE16" for an imgCIF or "BINARY" for a CBF. The octal, decimal and hexadecimal transfer encodings are for convenience in debugging, and are not recommended for archiving and data interchange. In an imgCIF file, the encoded binary data begins after the empty line terminating the header. In a CBF, the raw binary data begins after an empty line terminating the header and after the sequence: Octet Hex Decimal Purpose 0 0C 12 (ctrl-L) Page break 1 1A 26 (ctrl-Z) Stop listings in MS-DOS 2 04 04 (Ctrl-D) Stop listings in UNIX 3 D5 213 Binary section begins None of these octets are included in the calculation of the message size, nor in the calculation of the message digest. The X-Binary-Size header specifies the size of the equivalent binary data in octets. If compression was used, this size is the size after compression, including any book-keeping fields. An adjustment is made for the deprecated binary formats in which 8 bytes of binary header are used for the compression type. In that case, the 8 bytes used for the compression type is subtracted from the size, so that the same size will be reported if the compression type is supplied in the MIME header. Use of the MIME header is the recommended way to supply the compression type. In general, no portion of the binary header is included in the calculation of the size. The X-Binary-Element-Type header specifies the type of binary data in the octets, using the same descriptive phrases as in _array_structure.encoding_type. The default value is "unsigned 32-bit integer". An MD5 message digest may, optionally, be used. The "RSA Data Security, Inc. MD5 Message-Digest Algorithm" should be used. No portion of the header is included in the calculation of the message digest. If the Transfer Encoding is "X-BASE8", "X-BASE10", or "X-BASE16", the data is presented as octal, decimal or hexadecimal data organized into lines or words. Each word is created by composing octets of data in fixed groups of 2, 3, 4, 6 or 8 octets, either in the order ...4321 ("big- endian") or 1234... (little-endian). If there are fewer than the specified number of octets to fill the last word, then the missing octets are presented as "==" for each missing octet. Exactly two equal signs are used for each missing octet even for octal and decimal encoding. The format of lines is: rnd xxxxxx xxxxxx xxxxxx where r is "H", "O", or "D" for hexadecimal, octal or decimal, n is the number of octets per word. and d is "<" for ">" for the "...4321" and "1234..." octet orderings respectively. The "==" padding for the last word should be on the appropriate side to correspond to the missing octets, e.g. H4< FFFFFFFF FFFFFFFF 07FFFFFF ====0000 or H3> FF0700 00==== For these hex, octal and decimal formats, only, comments beginning with "#" are permitted to improve readability. BASE64 encoding follows MIME conventions. Octets are in groups of three, c1, c2, c3. The resulting 24 bits are broken into four 6-bit quantities, starting with the high-order six bits (c1 >> 2) of the first octet, then the low-order two bits of the first octet followed by the high-order 4 bits of the second octet ((c1 & 3)<<4 | (c2>>4)), then the bottom 4 bits of the second octet followed by the high order two bits of the last octet ((c2 & 15)<<2 | (c3>>6)), then the bottom six bits of the last octet (c3 & 63). Each of these four quantities is translated into an ASCII character using the mapping: 1 2 3 4 5 6 0123456789012345678901234567890123456789012345678901234567890123 | | | | | | | ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/ With short groups of octets padded on the right with one "=" if c3 is missing, and with "==" if both c2 and c3 are missing. QUOTED-PRINTABLE encoding also follows MIME conventions, copying octets without translation if their ASCII values are 32..38, 42, 48..57, 59..60, 62, 64..126 and the octet is not a ";" in column 1. All other characters are translated to =nn, where nn is the hexadecimal encoding of the octet. All lines are "wrapped" with a terminating "=" (i.e. the MIME conventions for an implicit line terminator are never used). ; _item.name '<a href="#_array_data.data" >_array_data.data</a>' _item.category_id array_data _item.mandatory_code yes _item_type.code binary save_ ###################### # <a name="ARRAY_ELEMENT_SIZE">ARRAY_ELEMENT_SIZE</a> # ###################### save_ARRAY_ELEMENT_SIZE _category.description ; Data items in the <a href="#ARRAY_ELEMENT_SIZE">ARRAY_ELEMENT_SIZE</a> 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 '<a href="#_array_element_size.array_id" >_array_element_size.array_id</a>' '<a href="#_array_element_size.index" >_array_element_size.index</a>' 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_ <a href="#_array_element_size.array_id" >_array_element_size.array_id</a> <a href="#_array_element_size.index" >_array_element_size.index</a> <a href="#_array_element_size.size" >_array_element_size.size</a> image_1 1 1.22e-6 image_1 2 1.22e-6 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save_<a name="_array_element_size.array_id" >_array_element_size.array_id</a> _item_description.description ; This item is a pointer to <a href="#_array_structure.id" >_array_structure.id</a> in the <a href="#ARRAY_STRUCTURE">ARRAY_STRUCTURE</a> category. ; _item.name '<a href="#_array_element_size.array_id" >_array_element_size.array_id</a>' _item.category_id array_element_size _item.mandatory_code yes _item_type.code code save_ save_<a name="_array_element_size.index" >_array_element_size.index</a> _item_description.description ; This item is a pointer to <a href="#_array_structure_list.index" >_array_structure_list.index</a> in the ARRAY_STRUCTURE_LIST category. ; _item.name '<a href="#_array_element_size.index" >_array_element_size.index</a>' _item.category_id array_element_size _item.mandatory_code yes _item_type.code code save_ save_<a name="_array_element_size.size" >_array_element_size.size</a> _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 '<a href="#_array_element_size.size" >_array_element_size.size</a>' _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_ ##################### # <a name="ARRAY_INTENSITIES">ARRAY_INTENSITIES</a> # ##################### save_ARRAY_INTENSITIES _category.description ; Data items in the <a href="#ARRAY_INTENSITIES">ARRAY_INTENSITIES</a> category record the information required to recover the intensity data from the set of data values stored in the <a href="#ARRAY_DATA">ARRAY_DATA</a> category. The actual 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 '<a href="#_array_intensities.array_id" >_array_intensities.array_id</a>' '<a href="#_array_intensities.binary_id" >_array_intensities.binary_id</a>' loop_ _category_group.id 'inclusive_group' 'array_data_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 ; ; loop_ <a href="#_array_intensities.array_id" >_array_intensities.array_id</a> <a href="#_array_intensities.linearity" >_array_intensities.linearity</a> <a href="#_array_intensities.gain" >_array_intensities.gain</a> <a href="#_array_intensities.overload" >_array_intensities.overload</a> <a href="#_array_intensities.undefined_value" >_array_intensities.undefined_value</a> image_1 linear 1.2 655535 0 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save_<a name="_array_intensities.array_id" >_array_intensities.array_id</a> _item_description.description ; This item is a pointer to <a href="#_array_structure.id" >_array_structure.id</a> in the <a href="#ARRAY_STRUCTURE">ARRAY_STRUCTURE</a> category. ; _item.name '<a href="#_array_intensities.array_id" >_array_intensities.array_id</a>' _item.category_id array_intensities _item.mandatory_code yes _item_type.code code save_ save_<a name="_array_intensities.binary_id" >_array_intensities.binary_id</a> _item_description.description ; This item is a pointer to <a href="#_array_data.binary_id" >_array_data.binary_id</a> in the <a href="#ARRAY_DATA">ARRAY_DATA</a> category. ; _item.name '<a href="#_array_intensities.binary_id" >_array_intensities.binary_id</a>' _item.category_id array_intensities _item.mandatory_code implicit _item_type.code int save_ save_<a name="_array_intensities.gain" >_array_intensities.gain</a> _item_description.description ; Detector "gain". The factor by which linearized intensity count values should be divided to produce true photon counts. ; _item.name '<a href="#_array_intensities.gain" >_array_intensities.gain</a>' _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 '<a href="#_array_intensities.gain_esd" >_array_intensities.gain_esd</a>' 'associated_value' save_ save_<a name="_array_intensities.gain_esd" >_array_intensities.gain_esd</a> _item_description.description ; The estimated standard deviation in detector "gain". ; _item.name '<a href="#_array_intensities.gain_esd" >_array_intensities.gain_esd</a>' _item.category_id array_intensities _item.mandatory_code yes _item_type.code float _item_units.code 'counts_per_photon' loop_ _item_related.related_name _item_related.function_code '<a href="#_array_intensities.gain" >_array_intensities.gain</a>' 'associated_esd' save_ save_<a name="_array_intensities.linearity" >_array_intensities.linearity</a> _item_description.description ; The intensity linearity scaling used from raw intensity to the stored element value: 'linear' is obvious 'offset' means that the value defined by '<a href="#_array_intensities.offset" >_array_intensities.offset</a>' should be added to each element value. 'scaling' means that the value defined by '_array_intensities.scaling' should be multiplied with each element value. 'scaling_offset' is the combination of the two previous cases, with the scale factor applied before the offset value. 'sqrt_scaled' means that the square root of raw intensities multiplied by '_array_intensities.scaling' is calculated and stored, perhaps rounded to the nearest integer. Thus, linearization involves dividing the stored values by '_array_intensities.scaling' and squaring the result. 'logarithmic_scaled' means that the logarithm based 10 of raw intensities multiplied by '_array_intensities.scaling' is calculated and stored, perhaps rounded to the nearest integer. Thus, linearization involves dividing the stored values by '_array_intensities.scaling' and calculating 10 to the power of this number. 'raw' means that the data is the raw is a set of raw values straight from the detector. ; _item.name '<a href="#_array_intensities.linearity" >_array_intensities.linearity</a>' _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 '<a href="#_array_intensities.offset" >_array_intensities.offset</a>' should be added to each element value. ; 'scaling' ; The value defined by '<A HREF="#_array_intensities.scaling">_array_intensities.scaling</A>' 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 '<A HREF="#_array_intensities.scaling">_array_intensities.scaling</A>' is calculated and stored, perhaps rounded to the nearest integer. Thus, linearization involves dividing the stored values by '<A HREF="#_array_intensities.scaling">_array_intensities.scaling</A>' and squaring the result. ; 'logarithmic_scaled' ; The logarithm based 10 of raw intensities multiplied by '<A HREF="#_array_intensities.scaling">_array_intensities.scaling</A>' is calculated and stored, perhaps rounded to the nearest integer. Thus, linearization involves dividing the stored values by '<A HREF="#_array_intensities.scaling">_array_intensities.scaling</A>' 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_<a name="_array_intensities.offset" >_array_intensities.offset</a> _item_description.description ; Offset value to add to array element values in the manner described by item <a href="#_array_intensities.linearity" >_array_intensities.linearity</a>. ; _item.name '<a href="#_array_intensities.offset" >_array_intensities.offset</a>' _item.category_id array_intensities _item.mandatory_code no _item_type.code float save_ save_<a name="_array_intensities.scaling" >_array_intensities.scaling</a> _item_description.description ; Multiplicative scaling value to be applied to array data in the manner described by item <a href="#_array_intensities.linearity" >_array_intensities.linearity</a>. ; _item.name '<a href="#_array_intensities.scaling" >_array_intensities.scaling</a>' _item.category_id array_intensities _item.mandatory_code no _item_type.code float save_ save_<a name="_array_intensities.overload" >_array_intensities.overload</a> _item_description.description ; The saturation intensity level for this data array. ; _item.name '<a href="#_array_intensities.overload" >_array_intensities.overload</a>' _item.category_id array_intensities _item.mandatory_code no _item_type.code float _item_units.code 'counts' save_ save_<a name="_array_intensities.undefined_value" >_array_intensities.undefined_value</a> _item_description.description ; A value to be substituted for undefined values in the data array. ; _item.name '<a href="#_array_intensities.undefined_value" >_array_intensities.undefined_value</a>' _item.category_id array_intensities _item.mandatory_code no _item_type.code float save_ ################### # <a name="ARRAY_STRUCTURE">ARRAY_STRUCTURE</a> # ################### save_ARRAY_STRUCTURE _category.description ; Data items in the <a href="#ARRAY_STRUCTURE">ARRAY_STRUCTURE</a> category record the organization and encoding of array data which may be stored in the <a href="#ARRAY_DATA">ARRAY_DATA</a> category. ; _category.id array_structure _category.mandatory_code no _category_key.name '<a href="#_array_structure.id" >_array_structure.id</a>' 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_<a name="_array_structure.byte_order" >_array_structure.byte_order</a> _item_description.description ; The order of bytes for integer values which require more than 1-byte. (IBM-PC's and compatibles, and Dec-Vaxes use low-byte-first ordered integers, whereas Hewlett Packard 700 series, Sun-4 and Silicon Graphics use high-byte-first ordered integers. Dec-Alphas can produce/use either depending on a compiler switch.) ; _item.name '<a href="#_array_structure.byte_order" >_array_structure.byte_order</a>' _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_<a name="_array_structure.compression_type" >_array_structure.compression_type</a> _item_description.description ; Type of data compression method used to compress the array data. ; _item.name '<a href="#_array_structure.compression_type" >_array_structure.compression_type</a>' _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 '<a href="#_array_structure.encoding_type" >_array_structure.encoding_type</a>' and '<a href="#_array_structure.byte_order" >_array_structure.byte_order</a>'. ; 'byte_offsets' ; Using the compression scheme defined in CBF definition Section 5.0. ; 'packed' ; Using the 'packed' compression scheme, a CCP4-style packing (CBFlib section 3.3.2) ; 'canonical' ; Using the 'canonical' compression scheme (CBFlib section 3.3.1) ; save_ save_<a name="_array_structure.encoding_type" >_array_structure.encoding_type</a> _item_description.description ; Data encoding of a single element of array data. In several cases, the IEEE format is referenced. See "IEEE Standard for Binary Floating-Point Arithmetic", ANSI/IEEE Std 754-1985, the Institute of Electrical and Electronics Engineers, Inc., NY 1985. ; _item.name '<a href="#_array_structure.encoding_type" >_array_structure.encoding_type</a>' _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_<a name="_array_structure.id" >_array_structure.id</a> _item_description.description ; The value of <a href="#_array_structure.id" >_array_structure.id</a> must uniquely identify each item of array data. ; loop_ _item.name _item.category_id _item.mandatory_code '<a href="#_array_structure.id" >_array_structure.id</a>' array_structure yes '<a href="#_array_data.array_id" >_array_data.array_id</a>' array_data yes '<a href="#_array_structure_list.array_id" >_array_structure_list.array_id</a>' array_structure_list yes '<a href="#_array_intensities.array_id" >_array_intensities.array_id</a>' array_intensities yes '<a href="#_diffrn_data_frame.array_id" >_diffrn_data_frame.array_id</a>' diffrn_data_frame yes _item_type.code code loop_ _item_linked.child_name _item_linked.parent_name '<a href="#_array_data.array_id" >_array_data.array_id</a>' '<a href="#_array_structure.id" >_array_structure.id</a>' '<a href="#_array_structure_list.array_id" >_array_structure_list.array_id</a>' '<a href="#_array_structure.id" >_array_structure.id</a>' '<a href="#_array_intensities.array_id" >_array_intensities.array_id</a>' '<a href="#_array_structure.id" >_array_structure.id</a>' '<a href="#_diffrn_data_frame.array_id" >_diffrn_data_frame.array_id</a>' '<a href="#_array_structure.id" >_array_structure.id</a>' save_ ######################## # <a name="ARRAY_STRUCTURE_LIST">ARRAY_STRUCTURE_LIST</a> # ######################## save_ARRAY_STRUCTURE_LIST _category.description ; Data items in the <a href="#ARRAY_STRUCTURE_LIST">ARRAY_STRUCTURE_LIST</a> 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 '<a href="#_array_structure_list.array_id" >_array_structure_list.array_id</a>' '<a href="#_array_structure_list.index" >_array_structure_list.index</a>' loop_ _category_group.id 'inclusive_group' 'array_data_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - An image array of 1300 x 1200 elements. The raster order of the image is left-to-right (increasing) in first dimension and bottom-to-top (decreasing) in the second dimension. ; ; loop_ <a href="#_array_structure_list.array_id" >_array_structure_list.array_id</a> <a href="#_array_structure_list.index" >_array_structure_list.index</a> <a href="#_array_structure_list.dimension" >_array_structure_list.dimension</a> <a href="#_array_structure_list.precedence" >_array_structure_list.precedence</a> <a href="#_array_structure_list.direction" >_array_structure_list.direction</a> <a href="#_array_structure_list.axis_id" >_array_structure_list.axis_set_id</a> image_1 1 1300 1 increasing ELEMENT_X image_1 2 1200 2 decreasing ELEMENY_Y ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save_<a name="_array_structure_list.array_id" >_array_structure_list.array_id</a> _item_description.description ; This item is a pointer to <a href="#_array_structure.id" >_array_structure.id</a> in the <a href="#ARRAY_STRUCTURE">ARRAY_STRUCTURE</a> category. ; _item.name '<a href="#_array_structure_list.array_id" >_array_structure_list.array_id</a>' _item.category_id array_structure_list _item.mandatory_code yes _item_type.code code save_ save_<a name="_array_structure_list.axis_set_id" >_array_structure_list.axis_set_id</a> _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 <a href="#DIFFRN_DETECTOR_AXIS">DIFFRN_DETECTOR_AXIS</a>, but usually differ in that the axes in this category are the axes of the coordinate system of reported data points, while the axes in <a href="#DIFFRN_DETECTOR_AXIS">DIFFRN_DETECTOR_AXIS</a> 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 '<a href="#_array_structure_list.axis_set_id" >_array_structure_list.axis_set_id</a>' array_structure_list yes '<a href="#_array_structure_list_axis.axis_set_id" >_array_structure_list_axis.axis_set_id</a>' array_structure_list_axis implicit _item_type.code code loop_ _item_linked.child_name _item_linked.parent_name '<a href="#_array_structure_list_axis.axis_set_id" >_array_structure_list_axis.axis_set_id</a>' '<a href="#_array_structure_list.axis_set_id" >_array_structure_list.axis_set_id</a>' save_ save_<a name="_array_structure_list.dimension" >_array_structure_list.dimension</a> _item_description.description ; The number of elements stored in the array structure in this dimension. ; _item.name '<a href="#_array_structure_list.dimension" >_array_structure_list.dimension</a>' _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_<a name="_array_structure_list.direction" >_array_structure_list.direction</a> _item_description.description ; Identifies the direction in which this array index changes. ; _item.name '<a href="#_array_structure_list.direction" >_array_structure_list.direction</a>' _item.category_id array_structure_list _item.mandatory_code yes _item_type.code int loop_ _item_enumeration.value _item_enumeration.detail 'increasing' ; Indicates the index changes from 1 to the maximum dimension. ; 'decreasing' ; Indicates the index changes from the maximum dimension to 1. ; save_ save_<a name="_array_structure_list.index" >_array_structure_list.index</a> _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 '<a href="#_array_structure_list.index" >_array_structure_list.index</a>' array_structure_list yes '<a href="#_array_structure_list.precedence" >_array_structure_list.precedence</a>' array_structure_list yes '<a href="#_array_element_size.index" >_array_element_size.index</a>' array_element_size yes _item_type.code int loop_ _item_linked.child_name _item_linked.parent_name '<a href="#_array_element_size.index" >_array_element_size.index</a>' '<a href="#_array_structure_list.index" >_array_structure_list.index</a>' loop_ _item_range.maximum _item_range.minimum 1 1 . 1 save_ save_<a name="_array_structure_list.precedence" >_array_structure_list.precedence</a> _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 '<a href="#_array_structure_list.precedence" >_array_structure_list.precedence</a>' _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_ ############################# # <a name="ARRAY_STRUCTURE_LIST_AXIS">ARRAY_STRUCTURE_LIST_AXIS</a> # ############################# save_ARRAY_STRUCTURE_LIST_AXIS _category.description ; Data items in the <a href="#ARRAY_STRUCTURE_LIST_AXIS">ARRAY_STRUCTURE_LIST_AXIS</a> category describe the physical settings of sets axes for the centres of pixels that correspond to data points described in the <a href="#ARRAY_STRUCTURE_LIST">ARRAY_STRUCTURE_LIST</a> 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 axis, one for the angular direction, 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 '<a href="#_array_structure_list_axis.axis_set_id" >_array_structure_list_axis.axis_set_id</a>' '<a href="#_array_structure_list_axis.axis_id" >_array_structure_list_axis.axis_id</a>' loop_ _category_group.id 'inclusive_group' 'array_data_group' save_ save_<a name="_array_structure_list_axis.axis_id" >_array_structure_list_axis.axis_id</a> _item_description.description ; The value of this data item is the identifier of one of the axes for the set of axes for which settings are being specified. Multiple axes may be specified for the same value of '<a href="#_array_structure_list_axis.axis_set_id" >_array_structure_list_axis.axis_set_id</a>' This item is a pointer to <a href="#_axis.id" >_axis.id</a> in the <a href="#AXIS">AXIS</a> category. ; _item.name '<a href="#_array_structure_list_axis.axis_id" >_array_structure_list_axis.axis_id</a>' _item.category_id array_structure_list_axis _item.mandatory_code yes save_ save_<a name="_array_structure_list_axis.axis_set_id" >_array_structure_list_axis.axis_set_id</a> _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 <a href="#_array_structure_list_axis.axis_set_id" >_array_structure_list_axis.axis_set_id</a> . This item is a pointer to <a href="#_array_structure_list.axis_set_id" >_array_structure_list.axis_set_id</a> in the <a href="#ARRAY_STRUCTURE_LIST">ARRAY_STRUCTURE_LIST</a> category. If this item is not specified, it defaults to the corresponding axis identifier. ; _item.name '<a href="#_array_structure_list_axis.axis_set_id" >_array_structure_list_axis.axis_set_id</a>' _item.category_id array_structure_list_axis _item.mandatory_code implicit save_ save_<a name="_array_structure_list_axis.angle" >_array_structure_list_axis.angle</a> _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 center of the pixel with index value 1. If the index is specified as 'decreasing' this will be the center of the pixel with maximum index value. ; _item.name '<a href="#_array_structure_list_axis.angle" >_array_structure_list_axis.angle</a>' _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_<A NAME="_array_structure_list_axis.angle_increment">_array_structure_list_axis.angle_increment</A> _item_description.description ; The pixel-center-to-pixel-center 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 in that case. See '<a href="#_array_structure_list_axis.angular_pitch">_array_structure_list_axis.angular_pitch</a>'. ; _item.name '<A HREF="#_array_structure_list_axis.angle_increment">_array_structure_list_axis.angle_increment</A>' _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_<a name="_array_structure_list_axis.displacement" >_array_structure_list_axis.displacement</a> _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 center of the pixel with index value 1. If the index is specified as 'decreasing' this will be the center of the pixel with maximum index value. ; _item.name '<a href="#_array_structure_list_axis.displacement" >_array_structure_list_axis.displacement</a>' _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_<A NAME="_array_structure_list_axis.displacement_increment">_array_structure_list_axis.displacement_increment</A> _item_description.description ; The pixel-center-to-pixel-center increment for the displacement setting of the specified axis in millimetres. ; _item.name '<A HREF="#_array_structure_list_axis.displacement_increment">_array_structure_list_axis.displacement_increment</A>' _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_<A NAME="_array_structure_list_axis.angular_pitch">_array_structure_list_axis.angular_pitch</A> _item_description.description ; The pixel-center-to-pixel-center 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 scan) and should not be specified for cases in which the angle between pixels, rather than the distance between pixels is uniform. See '<A HREF="_array_structure_list_axis.angle_increment">_array_structure_list_axis.angle_increment</A>'. ; _item.name '<A HREF="#_array_structure_list_axis.angular_pitch">_array_structure_list_axis.angular_pitch</A>' _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_<A NAME="_array_structure_list_axis.radial_pitch">_array_structure_list_axis.radial_pitch</A> _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 '<a href="#_array_structure_list_axis.displacement_increment">_array_structure_list_axis.displacement_increment</a>'. ; _item.name '<A HREF="#_array_structure_list_axis.radial_pitch">_array_structure_list_axis.radial_pitch</A>' _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_ ######## # <a name="AXIS">AXIS</a> # ######## save_AXIS _category.description ; Data items in the <a href="#AXIS">AXIS</a> 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 (Andrew G.W. Leslie, Harry Powell, MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH,UK <A HREF="http://www.dl.ac.uk/CCP/CCP4/dist/x-windows/Mosflm/">http://www.dl.ac.uk/CCP/CCP4/dist/x-windows/Mosflm/</A>). In MOSFLM, X is along the X-ray beam (our 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 center. The location of the beam center on the detector should be given in the <A HREF="#DIFFRN_DETECTOR">DIFFRN_DETECTOR</A> category in distortion-corrected mm from the (0,0) corner of the detector. It should be noted that many different origins arise in the definition of an experiment. In particular, as noted above, we need to specify the location of the beam center on the detector in terms of the origin of the detector, which is, of course, not coincident with the center of the sample. ; _category.id axis _category.mandatory_code no loop_ _category_key.name '<a href="#_axis.id" >_axis.id</a>' '_axis.equipment' loop_ _category_group.id 'inclusive_group' 'axis_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - This example shows the axis specification of the axes of a kappa geometry goniometer (See "X-Ray Structure Determination, A Practical Guide", 2nd ed. by G. H. Stout, L. H. Jensen, Wiley Interscience, 1989, 453 pp, p 134.). There are three axes specified, and no offsets. The outermost axis, omega, is pointed along the X-axis. The next innermost axis, kappa, is at a 50 degree angle to the X-axis, pointed away from the source. The innermost axis, phi, aligns with the X-axis when omega and phi are at their zero-points. If T-omega, T-kappa and T-phi are the transformation matrices derived from the axis settings, the complete transformation would be: x' = (T-omega) (T-kappa) (T-phi) x ; ; loop_ <a href="#_axis.id" >_axis.id</a> <a href="#_axis.type" >_axis.type</a> <a href="#_axis.equipment" >_axis.equipment</a> <a href="#_axis.depends_on" >_axis.depends_on</a> <a href="#_axis.vector[1]" >_axis.vector[1]</a> <a href="#_axis.vector[2]" >_axis.vector[2]</a> <a href="#_axis.vector[3]" >_axis.vector[3]</a> omega rotation goniometer . 1 0 0 kappa rotation goniometer omega -.64279 0 -.76604 phi rotation goniometer kappa 1 0 0 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - This example show the axis specification of the axes of a detector, source and gravity. We have juggled the order as a reminder that the ordering of presentation of tokens is not significant. We have taken the center of rotation of the detector to be 68 millimetres in the direction away from the source. ; ; loop_ <a href="#_axis.id" >_axis.id</a> <a href="#_axis.type" >_axis.type</a> <a href="#_axis.equipment" >_axis.equipment</a> <a href="#_axis.depends_on" >_axis.depends_on</a> <a href="#_axis.vector[1]" >_axis.vector[1]</a> <a href="#_axis.vector[2]" >_axis.vector[2]</a> <a href="#_axis.vector[3]" >_axis.vector[3]</a> <A HREF="#_axis.offset[1]">_axis.offset[1]</A> <A HREF="#_axis.offset[2]">_axis.offset[2]</A> <A HREF="#_axis.offset[3]">_axis.offset[3]</A> 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_<a name="_axis.depends_on" >_axis.depends_on</a> _item_description.description ; The value of <a href="#_axis.type" >_axis.type</a></a> specifies the next outermost axis upon which this axis depends. This item is a pointer to axis.id in the same category. ; _item.name '<A HREF="#_axis.depends_on">_axis.depends_on</A>' _item.category_id axis _item.mandatory_code no save_ save_<a name="_axis.equipment" >_axis.equipment</a> _item_description.description ; The value of <a href="#_axis.type" >_axis.type</a></a> specifies the type of equipment using the axis: goniometer, detector, gravity, source or general ; _item.name '<A HREF="#_axis.equipment">_axis.equipment</A>' _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_<a name="_axis.offset[1]" >_axis.offset[1]</a> _item_description.description ; The [1] element of the 3-element vector used to specify the offset to the base of a rotation or translation axis. The vector is specified in millimetres ; _item.name '<A HREF="#_axis.offset[1]">_axis.offset[1]</A>' _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_<a name="_axis.offset[2]" >_axis.offset[2]</a> _item_description.description ; The [2] element of the 3-element vector used to specify the offset to the base of a rotation or translation axis. The vector is specified in millimetres ; _item.name '<A HREF="#_axis.offset[2]">_axis.offset[2]</A>' _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_<a name="_axis.offset[3]" >_axis.offset[3]</a> _item_description.description ; The [3] element of the 3-element vector used to specify the offset to the base of a rotation or translation axis. The vector is specified in millimetres ; _item.name '<A HREF="#_axis.offset[3]">_axis.offset[3]</A>' _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_<a name="_axis.id" >_axis.id</a></a> _item_description.description ; The value of <a href="#_axis.id" >_axis.id</a> must uniquely identify each axis relevant to the experiment. Note that multiple pieces of equipment may share the same axis (e.g. a twotheta arm), so that the category key for <a href="#AXIS">AXIS</a> also includes the equipment. ; loop_ _item.name _item.category_id _item.mandatory_code '<a href="#_axis.id" >_axis.id</a>' axis yes '<a href="#_array_structure_list_axis.axis_id" >_array_structure_list_axis.axis_id</a>' array_structure_list_axis yes '<a href="#_diffrn_detector_axis.axis_id" >_diffrn_detector_axis.axis_id</a>' diffrn_detector_axis yes '<a href="#_diffrn_measurement_axis.axis_id" >_diffrn_measurement_axis.axis_id</a>' diffrn_measurement_axis yes '<a href="#_diffrn_scan_axis.axis_id" >_diffrn_scan_axis.axis_id</a>' diffrn_scan_axis yes '<a href="#_diffrn_scan_frame_axis.axis_id" >_diffrn_scan_frame_axis.axis_id</a>' diffrn_scan_frame_axis yes _item_type.code code loop_ _item_linked.child_name _item_linked.parent_name '<a href="#_axis.depends_on" >_axis.depends_on</a>' '<a href="#_axis.id" >_axis.id</a>' '<a href="#_array_structure_list_axis.axis_id" >_array_structure_list_axis.axis_id</a>' '<a href="#_axis.id" >_axis.id</a>' '<a href="#_diffrn_detector_axis.axis_id" >_diffrn_detector_axis.axis_id</a>' '<a href="#_axis.id" >_axis.id</a>' '<a href="#_diffrn_measurement_axis.axis_id" >_diffrn_measurement_axis.axis_id</a>' '<a href="#_axis.id" >_axis.id</a>' '<a href="#_diffrn_scan_axis.axis_id" >_diffrn_scan_axis.axis_id</a>' '<a href="#_axis.id" >_axis.id</a>' '<a href="#_diffrn_scan_frame_axis.axis_id" >_diffrn_scan_frame_axis.axis_id</a>' '<a href="#_axis.id" >_axis.id</a>' save_ save_<a name="_axis.type" >_axis.type</a> _item_description.description ; The value of <a href="#_axis.type" >_axis.type</a></a> specifies the type of axis: rotation, translation (or general when the type is not relevant, as for gravity) ; _item.name '<A HREF="#_axis.type">_axis.type</A>' _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_<a name="_axis.vector[1]" >_axis.vector[1]</a> _item_description.description ; The [1] element of the 3-element vector used to specify the direction of a rotation or translation axis. The vector should be normalized to be a unit vector, and is dimensionless. ; _item.name '<a href="#_axis.vector[1]" >_axis.vector[1]</a>' _item.category_id axis _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save_<a name="_axis.vector[2]" >_axis.vector[2]</a> _item_description.description ; The [2] element of the 3-element vector used to specify the direction of a rotation or translation axis. The vector should be normalized to be a unit vector, and is dimensionless. ; _item.name '<a href="#_axis.vector[2]" >_axis.vector[2]</a>' _item.category_id axis _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save_<a name="_axis.vector[3]" >_axis.vector[3]</a> _item_description.description ; The [3] element of the 3-element vector used to specify the direction of a rotation or translation axis. The vector should be normalized to be a unit vector, and is dimensionless. ; _item.name '<a href="#_axis.vector[3]" >_axis.vector[3]</a>' _item.category_id axis _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ ##################### # <a name="DIFFRN_DATA_FRAME" >DIFFRN_DATA_FRAME</a> # ##################### save_DIFFRN_DATA_FRAME _category.description ; Data items in the <a href="#DIFFRN_DATA_FRAME">DIFFRN_DATA_FRAME</a> 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 '<a href="#_diffrn_data_frame.id" >_diffrn_data_frame.id</a>' '<a href="#_diffrn_data_frame.detector_element_id" >_diffrn_data_frame.detector_element_id</a>' 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 <a href="#ARRAY_STRUCTURE">ARRAY_STRUCTURE</a> and related categories. The data for each detector element is stored in four groups of binary data in the <a href="#ARRAY_DATA">ARRAY_DATA</a> category, linked by the array_id and binary_id ; ; loop_ <a href="#_diffrn_data_frame.id" >_diffrn_data_frame.id</a> <a href="#_diffrn_data_frame.detector_element_id" >_diffrn_data_frame.detector_element_id</a> <a href="#_diffrn_data_frame.array_id" >_diffrn_data_frame.array_id</a> <a href="#_diffrn_data_frame.binary_id" >_diffrn_data_frame.binary_id</a> 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_<a name="_diffrn_data_frame.array_id" >_diffrn_data_frame.array_id</a> _item_description.description ; This item is a pointer to <a href="#_array_structure.id" >_array_structure.id</a> in the <a href="#ARRAY_STRUCTURE">ARRAY_STRUCTURE</a> category. ; _item.name '<a href="#_diffrn_data_frame.array_id" >_diffrn_data_frame.array_id</a>' _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 1.0.00 _item_type.code code save_ save_<a name="_diffrn_data_frame.binary_id" >_diffrn_data_frame.binary_id</a> _item_description.description ; This item is a pointer to <a href="#_array_data.binary_id" >_array_data.binary_id</a> in the <a href="#ARRAY_DATA">ARRAY_DATA</a> category. ; _item.name '<a href="#_diffrn_data_frame.binary_id" >_diffrn_data_frame.binary_id</a>' _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_<a name="_diffrn_data_frame.detector_element_id" >_diffrn_data_frame.detector_element_id</a> _item_description.description ; This item is a pointer to _diffrn_detector_element.id in the <a href="#DIFFRN_DETECTOR_ELEMENT">DIFFRN_DETECTOR_ELEMENT</a> category. ; _item.name '<a href="#_diffrn_data_frame.detector_element_id" >_diffrn_data_frame.detector_element_id</a>' _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_<a name="_diffrn_data_frame.id" >_diffrn_data_frame.id</a> _item_description.description ; The value of <a href="#_diffrn_data_frame.id" >_diffrn_data_frame.id</a> must uniquely identify each complete frame of data. ; loop_ _item.name _item.category_id _item.mandatory_code '<a href="#_diffrn_data_frame.id" >_diffrn_data_frame.id</a>' diffrn_data_frame yes '<a href="#_diffrn_refln.frame_id" >_diffrn_refln.frame_id</a>' diffrn_refln yes '<a href="#_diffrn_scan.frame_id_start" >_diffrn_scan.frame_id_start</a>' diffrn_scan yes '<a href="#_diffrn_scan.frame_id_end" >_diffrn_scan.frame_id_end</a>' diffrn_scan yes '<a href="#_diffrn_scan_frame.frame_id" >_diffrn_scan_frame.frame_id</a>' diffrn_scan_frame yes '<a href="#_diffrn_scan_frame_axis.frame_id" >_diffrn_scan_frame_axis.frame_id</a>' 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 '<a href="#_diffrn_refln.frame_id" >_diffrn_refln.frame_id</a>' '<a href="#_diffrn_data_frame.id" >_diffrn_data_frame.id</a>' '<a href="#_diffrn_scan.frame_id_start" >_diffrn_scan.frame_id_start</a>' '<a href="#_diffrn_data_frame.id" >_diffrn_data_frame.id</a>' '<a href="#_diffrn_scan.frame_id_end" >_diffrn_scan.frame_id_end</a>' '<a href="#_diffrn_data_frame.id" >_diffrn_data_frame.id</a>' '<a href="#_diffrn_scan_frame.frame_id" >_diffrn_scan_frame.frame_id</a>' '<a href="#_diffrn_data_frame.id" >_diffrn_data_frame.id</a>' '<a href="#_diffrn_scan_frame_axis.frame_id" >_diffrn_scan_frame_axis.frame_id</a>' '<a href="#_diffrn_data_frame.id" >_diffrn_data_frame.id</a>' save_ ########################################################################## # The following is a restatement of the mmCIF <A HREF="#DIFFRN_DETECTOR">DIFFRN_DETECTOR</A>, # # <a href="#DIFFRN_MEASUREMENT">DIFFRN_MEASUREMENT</a> and <A HREF="#DIFFRN_RADIATION">DIFFRN_RADIATION</A> categories, modified for # # the CBF/imgCIF extensions # ########################################################################## ################### # <a name="DIFFRN_DETECTOR">DIFFRN_DETECTOR</a> # ################### save_DIFFRN_DETECTOR _category.description ; Data items in the <A HREF="#DIFFRN_DETECTOR">DIFFRN_DETECTOR</A> 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 '<a href="#_diffrn_detector.diffrn_id" >_diffrn_detector.diffrn_id</a>' '<a href="#_diffrn_detector.id" >_diffrn_detector.id</a>' 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 ; ; <a href="#_diffrn_detector.diffrn_id" >_diffrn_detector.diffrn_id</a> 'd1' <a href="#_diffrn_detector.detector" >_diffrn_detector.detector</a> 'multiwire' <a href="#_diffrn_detector.type" >_diffrn_detector.type</a> 'Siemens' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save_<a name="_diffrn_detector.details" >_diffrn_detector.details</a> _item_description.description ; A description of special aspects of the radiation detector. ; _item.name '<a href="#_diffrn_detector.details" >_diffrn_detector.details</a>' _item.category_id diffrn_detector _item.mandatory_code no _item_aliases.alias_name '_diffrn_detector_details' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case ; Need new example here. ; save_ save_<a name="_diffrn_detector.detector" >_diffrn_detector.detector</a> _item_description.description ; The general class of the radiation detector. ; _item.name '<a href="#_diffrn_detector.detector" >_diffrn_detector.detector</a>' _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_<a name="_diffrn_detector.diffrn_id" >_diffrn_detector.diffrn_id</a> _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 '<a href="#_diffrn_detector.diffrn_id" >_diffrn_detector.diffrn_id</a>' _item.mandatory_code yes save_ save_<a name="_diffrn_detector.dtime" >_diffrn_detector.dtime</a> _item_description.description ; The deadtime in microseconds of the detectors used to measure the diffraction intensities. ; _item.name '<a href="#_diffrn_detector.dtime" >_diffrn_detector.dtime</a>' _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_<a name="_diffrn_detector.id" >_diffrn_detector.id</a> _item_description.description ; The value of <a href="#_diffrn_detector.id" >_diffrn_detector.id</a> must uniquely identify each detector used to collect each diffraction data set. If the value of <a href="#_diffrn_detector.id" >_diffrn_detector.id</a> is not given, it is implicitly equal to the value of <a href="#_diffrn_detector.diffrn_id" >_diffrn_detector.diffrn_id</a> ; loop_ _item.name _item.category_id _item.mandatory_code '<a href="#_diffrn_detector.id" >_diffrn_detector.id</a>' diffrn_detector implicit '<a href="#_diffrn_detector_axis.detector_id" >_diffrn_detector_axis.detector_id</a>' diffrn_detector_axis yes loop_ _item_linked.child_name _item_linked.parent_name '<a href="#_diffrn_detector_axis.detector_id" >_diffrn_detector_axis.detector_id</a>' '_diffrn_detector.id' _item_type.code code save_ save_<a name="_diffrn_detector.number_of_axes" >_diffrn_detector.number_of_axes</a> _item_description.description ; The value of <a href="#_diffrn_detector.number_of_axes" >_diffrn_detector.number_of_axes</a> gives the number of axes of the positioner for the detector identified by <a href="#_diffrn_detector.id" >_diffrn_detector.id</a> 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 <a href="#DIFFRN_DETECTOR_AXIS">DIFFRN_DETECTOR_AXIS</a>. ; _item.name '<a href="#_diffrn_detector.number_of_axes" >_diffrn_detector.number_of_axes</a>' _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_<a name="_diffrn_detector.type" >_diffrn_detector.type</a> _item_description.description ; The make, model or name of the detector device used. ; _item.name '<a href="#_diffrn_detector.type" >_diffrn_detector.type</a>' _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_ ######################## # <a name="DIFFRN_DETECTOR_AXIS" >DIFFRN_DETECTOR_AXIS</a> # ######################## save_DIFFRN_DETECTOR_AXIS _category.description ; Data items in the <a href="#DIFFRN_DETECTOR_AXIS">DIFFRN_DETECTOR_AXIS</a> category associate axes with detectors. ; _category.id diffrn_detector_axis _category.mandatory_code no loop_ _category_key.name '<a href="#_diffrn_detector_axis.detector_id" >_diffrn_detector_axis.detector_id</a>' '_diffrn_detector_axis.axis_id' loop_ _category_group.id 'inclusive_group' 'diffrn_group' save_ save_<a name="_diffrn_detector_axis.axis_id" >_diffrn_detector_axis.axis_id</a> _item_description.description ; This data item is a pointer to <a href="#_axis.id" >_axis.id</a> in the AXIS category. ; _item.name '<A HREF="#_diffrn_detector_axis.axis_id">_diffrn_detector_axis.axis_id</A>' _item.category_id diffrn_detector_axis _item.mandatory_code yes _item_type.code code save_ save_<a name="_diffrn_detector_axis.detector_id" >_diffrn_detector_axis.detector_id</a> _item_description.description ; This data item is a pointer to <a href="#_diffrn_detector.id" >_diffrn_detector.id</a> in the <A HREF="#DIFFRN_DETECTOR">DIFFRN_DETECTOR</A> 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 '<a href="#_diffrn_detector_axis.detector_id" >_diffrn_detector_axis.detector_id</a>' _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 save_ ########################### # <a name="DIFFRN_DETECTOR_ELEMENT">DIFFRN_DETECTOR_ELEMENT</a> # ########################### save_DIFFRN_DETECTOR_ELEMENT _category.description ; Data items in the <a href="#DIFFRN_DETECTOR_ELEMENT">DIFFRN_DETECTOR_ELEMENT</a> category record the details about spatial layout and other characteristics of each element of a detector which may have multiple elements. In most cases, the more detailed information provided in <A HREF="#ARRAY_STRUCTURE_LIST">ARRAY_STRUCTURE_LIST</A> and <A HREF="#ARRAY_STRUCTURE_LIST_AXIS">ARRAY_STRUCTURE_LIST_AXIS</A> are preferable to simply providing the centre. ; _category.id diffrn_detector_element _category.mandatory_code no loop_ _category_key.name '<a href="#_diffrn_detector_element.id" >_diffrn_detector_element.id</a>' '<a href="#_diffrn_detector_element.detector_id" >_diffrn_detector_element.detector_id</a>' loop_ _category_group.id 'inclusive_group' 'array_data_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - Detector d1 is composed of four CCD detector elements, each 200 mm by 200 mm, arranged in a square. in the pattern 1 2 * 3 4 Note that the beam center is slightly off of each of the detector elements, just beyond the lower right corner of 1, the lower left corner of 2, the upper right corner of 3 and the upper left corner of 4. ; ; loop_ <a href="#_diffrn_detector_element.id" >_diffrn_detector_element.id</a> <a href="#_diffrn_detector_element.detector_id" >_diffrn_detector_element.detector_id</a> <a href="#_diffrn_detector_element.center[1]" >_diffrn_detector_element.center[1]</a> <a href="#_diffrn_detector_element.center[2]" >_diffrn_detector_element.center[2]</a> 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_<a name="_diffrn_detector_element.center[1]" >_diffrn_detector_element.center[1]</a> _item_description.description ; The value of <a href="#_diffrn_detector_element.center[1]" >_diffrn_detector_element.center[1]</a> is the X component of the distortion-corrected beam-center in mm from the (0, 0) (lower left) corner of the detector element viewed from the sample side. ; _item.name '<a href="#_diffrn_detector_element.center[1]" >_diffrn_detector_element.center[1]</a>' _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_<a name="_diffrn_detector_element.center[2]" >_diffrn_detector_element.center[2]</a> _item_description.description ; The value of <a href="#_diffrn_detector_element.center[2]" >_diffrn_detector_element.center[2]</a> is the Y component of the distortion-corrected beam-center in mm from the (0, 0) (lower left) corner of the detector element viewed from the sample side. ; _item.name '<a href="#_diffrn_detector_element.center[2]" >_diffrn_detector_element.center[2]</a>' _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_<a name="_diffrn_detector_element.id" >_diffrn_detector_element.id</a> _item_description.description ; The value of <a href="#_diffrn_detector_element.id" >_diffrn_detector_element.id</a> must uniquely identify each element of a detector. ; loop_ _item.name _item.category_id _item.mandatory_code '<a href="#_diffrn_detector_element.id" >_diffrn_detector_element.id</a>' diffrn_detector_element yes _item_type.code code loop_ _item_linked.child_name _item_linked.parent_name '<a href="#_diffrn_data_frame.detector_element_id" >_diffrn_data_frame.detector_element_id</a>' '<a href="#_diffrn_detector_element.id" >_diffrn_detector_element.id</a>' save_ save_<a name="_diffrn_detector_element.detector_id" >_diffrn_detector_element.detector_id</a> _item_description.description ; This item is a pointer to <a href="#_diffrn_detector.id" >_diffrn_detector.id</a> in the <A HREF="#DIFFRN_DETECTOR">DIFFRN_DETECTOR</A> category. ; _item.name '<a href="#_diffrn_detector_element.detector_id" >_diffrn_detector_element.detector_id</a>' _item.category_id diffrn_detector_element _item.mandatory_code yes _item_type.code code save_ ######################## ## <a name="DIFFRN_MEASUREMENT" >DIFFRN_MEASUREMENT</a> ## ######################## save_DIFFRN_MEASUREMENT _category.description ; Data items in the <a href="#DIFFRN_MEASUREMENT">DIFFRN_MEASUREMENT</a> 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 '<a href="#_diffrn_measurement.device" >_diffrn_measurement.device</a>' '<a href="#_diffrn_measurement.diffrn_id" >_diffrn_measurement.diffrn_id</a>' '<a href="#_diffrn_measurement.id" >_diffrn_measurement.id</a>' 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 ; ; <a href="#_diffrn_measurement.diffrn_id" >_diffrn_measurement.diffrn_id</a> 'd1' <a href="#_diffrn_measurement.device" >_diffrn_measurement.device</a> '3-circle camera' <a href="#_diffrn_measurement.device_type" >_diffrn_measurement.device_type</a> 'Supper model x' <a href="#_diffrn_measurement.device_details" >_diffrn_measurement.device_details</a> 'none' <a href="#_diffrn_measurement.method" >_diffrn_measurement.method</a> 'omega scan' <a href="#_diffrn_measurement.details" >_diffrn_measurement.details</a> ; Need new example here ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; <a href="#_diffrn_measurement.diffrn_id" >_diffrn_measurement.diffrn_id</a> 's1' <a href="#_diffrn_measurement.device_type" >_diffrn_measurement.device_type</a> 'Philips PW1100/20 diffractometer' <a href="#_diffrn_measurement.method" >_diffrn_measurement.method</a> 'theta/2theta (\q/2\q)' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save_<a name="_diffrn_measurement.device" >_diffrn_measurement.device</a> _item_description.description ; The general class of goniometer or device used to support and orient the specimen. If the value of <A HREF="#_diffrn_measurement.device">_diffrn_measurement.device</A> is not given, it is implicitly equal to the value of _diffrn_measurement.diffrn_id Either '<A HREF="#_diffrn_measurement.device">_diffrn_measurement.device</A>' or '<A HREF="#_diffrn_measurement.id">_diffrn_measurement.id</A>' may be used to link to other categories. If the experimental setup admits multiple devices, then '<A HREF="#_diffrn_measurement.id">_diffrn_measurement.id</A>' is used to provide a unique link. ; loop_ _item.name _item.category_id _item.mandatory_code '<A HREF="#_diffrn_measurement.device">_diffrn_measurement.device</A>' diffrn_measurement implicit '<A HREF="#_diffrn_measurement_axis.measurement_device">_diffrn_measurement_axis.measurement_device</A>' diffrn_measurement_axis implicit loop_ _item_linked.child_name _item_linked.parent_name '<A HREF="#_diffrn_measurement_axis.measurement_device">_diffrn_measurement_axis.measurement_device</A>' '_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_<a name="_diffrn_measurement.device_details" >_diffrn_measurement.device_details</a> _item_description.description ; A description of special aspects of the device used to measure the diffraction intensities. ; _item.name '<a href="#_diffrn_measurement.device_details" >_diffrn_measurement.device_details</a>' _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_<a name="_diffrn_measurement.device_type" >_diffrn_measurement.device_type</a> _item_description.description ; The make, model or name of the measurement device (goniometer) used. ; _item.name '<a href="#_diffrn_measurement.device_type" >_diffrn_measurement.device_type</a>' _item.category_id diffrn_measurement _item.mandatory_code no _item_aliases.alias_name '_diffrn_measurement_device_type' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case 'Supper model q' 'Huber model r' 'Enraf-Nonius model s' 'homemade' save_ save_<a name="_diffrn_measurement.diffrn_id" >_diffrn_measurement.diffrn_id</a> _item_description.description ; This data item is a pointer to _diffrn.id in the DIFFRN category. ; _item.name '<a href="#_diffrn_measurement.diffrn_id" >_diffrn_measurement.diffrn_id</a>' _item.mandatory_code yes save_ save_<a name="_diffrn_measurement.details" >_diffrn_measurement.details</a> _item_description.description ; A description of special aspects of the intensity measurement. ; _item.name '<a href="#_diffrn_measurement.details" >_diffrn_measurement.details</a>' _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_<a name="_diffrn_measurement.id" >_diffrn_measurement.id</a> _item_description.description ; The value of <a href="#_diffrn_measurement.id" >_diffrn_measurement.id</a> must uniquely identify the set of mechanical characteristics of the device used to orient and/or position the sample used during collection of each diffraction data set. If the value of <a href="#_diffrn_measurement.id" >_diffrn_measurement.id</a> is not given, it is implicitly equal to the value of <a href="#_diffrn_measurement.diffrn_id" >_diffrn_measurement.diffrn_id</a> Either '<A HREF="#_diffrn_measurement.device">_diffrn_measurement.device</A>' or '<A HREF="#_diffrn_measurement.id">_diffrn_measurement.id</A>' may be used to link to other categories. If the experimental setup admits multiple devices, then '<A HREF="#_diffrn_measurement.id">_diffrn_measurement.id</A>' is used to provide a unique link. ; loop_ _item.name _item.category_id _item.mandatory_code '<a href="#_diffrn_measurement.id" >_diffrn_measurement.id</a>' diffrn_measurement implicit '<a href="#_diffrn_measurement_axis.measurement_id" >_diffrn_measurement_axis.measurement_id</a>' diffrn_measurement_axis implicit loop_ _item_linked.child_name _item_linked.parent_name '<a href="#_diffrn_measurement_axis.measurement_id" >_diffrn_measurement_axis.measurement_id</a>' '<a href="#_diffrn_measurement.id" >_diffrn_measurement.id</a>' _item_type.code code save_ save_<a name="_diffrn_measurement.method" >_diffrn_measurement.method</a> _item_description.description ; Method used to measure intensities. ; _item.name '<a href="#_diffrn_measurement.method" >_diffrn_measurement.method</a>' _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_<a name="_diffrn_measurement.number_of_axes" >_diffrn_measurement.number_of_axes</a> _item_description.description ; The value of <a href="#_diffrn_measurement.number_of_axes" >_diffrn_measurement.number_of_axes</a> gives the number of axes of the positioner for the goniometer or other sample orientation or positioning device identified by <a href="#_diffrn_measurement.id" >_diffrn_measurement.id</a> The description of the axes should be provided by entries in <a href="#DIFFRN_MEASUREMENT_AXIS">DIFFRN_MEASUREMENT_AXIS</a>. ; _item.name '<a href="#_diffrn_measurement.number_of_axes" >_diffrn_measurement.number_of_axes</a>' _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_<a name="_diffrn_measurement.specimen_support" >_diffrn_measurement.specimen_support</a> _item_description.description ; The physical device used to support the crystal during data collection. ; _item.name '<a href="#_diffrn_measurement.specimen_support" >_diffrn_measurement.specimen_support</a>' _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_ ########################### # <a name="DIFFRN_MEASUREMENT_AXIS">DIFFRN_MEASUREMENT_AXIS</a> # ########################### save_DIFFRN_MEASUREMENT_AXIS _category.description ; Data items in the <a href="#DIFFRN_MEASUREMENT_AXIS">DIFFRN_MEASUREMENT_AXIS</a> category associate axes with goniometers. ; _category.id diffrn_measurement_axis _category.mandatory_code no loop_ _category_key.name '<a href="#_diffrn_measurement_axis.measurement_device" >_diffrn_measurement_axis.measurement_device</a>' '<a href="#_diffrn_measurement_axis.measurement_id" >_diffrn_measurement_axis.measurement_id</a>' '<a href="#_diffrn_measurement_axis.axis_id" >_diffrn_measurement_axis.axis_id</a>' loop_ _category_group.id 'inclusive_group' 'diffrn_group' save_ save_<a name="_diffrn_measurement_axis.axis_id" >_diffrn_measurement_axis.axis_id</a> _item_description.description ; This data item is a pointer to <a href="#_axis.id" >_axis.id</a> in the <a href="#AXIS">AXIS</a> category. ; _item.name '<a href="#_diffrn_measurement_axis.axis_id" >_diffrn_measurement_axis.axis_id</a>' _item.category_id diffrn_measurement_axis _item.mandatory_code yes _item_type.code code save_ save_<A name="_diffrn_measurement_axis.measurement_device">_diffrn_measurement_axis.measurement_device</A> _item_description.description ; This data item is a pointer to <A HREF="#_diffrn_measurement.device">_diffrn_measurement.device</A> in the <a href="#DIFFRN_MEASUREMENT">DIFFRN_MEASUREMENT</a> category. ; _item.name '<A HREF="#_diffrn_measurement_axis.measurement_device">_diffrn_measurement_axis.measurement_device</A>' _item.category_id diffrn_measurement_axis _item.mandatory_code implicit save_ save_<A NAME="_diffrn_measurement_axis.measurement_id">_diffrn_measurement_axis.measurement_id</A> _item_description.description ; This data item is a pointer to <A HREF="#_diffrn_measurement.id">_diffrn_measurement.id</A> in the <a href="#DIFFRN_MEASUREMENT">DIFFRN_MEASUREMENT</a> 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 '<A HREF="#_diffrn_measurement_axis.measurement_id">_diffrn_measurement_axis.measurement_id</A>' _item.category_id diffrn_measurement_axis _item_aliases.alias_name '_diffrn_measurement_axis.id' _item_aliases.dictionary cif_img.dic _item_aliases.version 1.0.00 _item.mandatory_code implicit save_ #################### # <A NAME="DIFFRN_RADIATION">DIFFRN_RADIATION</A> # #################### save_DIFFRN_RADIATION _category.description ; Data items in the <A HREF="#DIFFRN_RADIATION">DIFFRN_RADIATION</A> category describe the radiation used in measuring diffraction intensities, its collimation and monochromatisation before the sample. Post-sample treatment of the beam is described by data items in the <A HREF="#DIFFRN_DETECTOR">DIFFRN_DETECTOR</A> category. ; _category.id diffrn_radiation _category.mandatory_code no _category_key.name '<A HREF="#_diffrn_radiation.diffrn_id">_diffrn_radiation.diffrn_id</A>' 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 ; ; <A HREF="#_diffrn_radiation.diffrn_id">_diffrn_radiation.diffrn_id</A> 'set1' <A HREF="#_diffrn_radiation.collimation">_diffrn_radiation.collimation</A> '0.3 mm double pinhole' <A HREF="#_diffrn_radiation.monochromator">_diffrn_radiation.monochromator</A> 'graphite' <A HREF="#_diffrn_radiation.type">_diffrn_radiation.type</A> 'Cu K\a' <A HREF="#_diffrn_radiation.wavelength_id">_diffrn_radiation.wavelength_id</A> 1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; <A HREF="#_diffrn_radiation.wavelength_id">_diffrn_radiation.wavelength_id</A> 1 <A HREF="#_diffrn_radiation.type">_diffrn_radiation.type</A> 'Cu K\a' <A HREF="#_diffrn_radiation.monochromator">_diffrn_radiation.monochromator</A> 'graphite' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save_<A name="_diffrn_radiation.collimation">_diffrn_radiation.collimation</A> _item_description.description ; The collimation or focusing applied to the radiation. ; _item.name '<A HREF="#_diffrn_radiation.collimation">_diffrn_radiation.collimation</A>' _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_<A name="_diffrn_radiation.diffrn_id">_diffrn_radiation.diffrn_id</A> _item_description.description ; This data item is a pointer to _diffrn.id in the DIFFRN category. ; _item.name '<A HREF="#_diffrn_radiation.diffrn_id">_diffrn_radiation.diffrn_id</A>' _item.mandatory_code yes save_ save_<A NAME="_diffrn_radiation.div_x_source">_diffrn_radiation.div_x_source</A> _item_description.description ; Beam crossfire in degrees parallel to the laboratory X axis (see <a href="#AXIS">AXIS</a> category). This is a characteristic of the xray beam as it illuminates the sample (or specimen) after all monochromation and collimation. This is the esd of the directions of photons in the X-Z plane around the mean source beam direction. Note that some synchrotrons specify this value in milliradians, in which case a conversion would be needed. To go from a value in milliradians to a value in degrees, multiply by 0.180 and divide by Pi. ; _item.name '<A HREF="#_diffrn_radiation.div_x_source">_diffrn_radiation.div_x_source</A>' _item.category_id diffrn_radiation _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save_<A name="_diffrn_radiation.div_y_source">_diffrn_radiation.div_y_source</A> _item_description.description ; Beam crossfire in degrees parallel to the laboratory Y axis (see <a href="#AXIS">AXIS</a> category). This is a characteristic of the xray beam as it illuminates the sample (or specimen) after all monochromation and collimation. This is the esd of the directions of photons in the Y-Z plane around the mean source beam direction. Note that some synchrotrons specify this value in milliradians, in which case a conversion would be needed. To go from a value in milliradians to a value in degrees, multiply by 0.180 and divide by Pi. ; _item.name '<A HREF="#_diffrn_radiation.div_y_source">_diffrn_radiation.div_y_source</A>' _item.category_id diffrn_radiation _item.mandatory_code no _item_type.code float _item_units.code degrees _item_default.value 0.0 save_ save_<A name="_diffrn_radiation.div_x_y_source">_diffrn_radiation.div_x_y_source</A> _item_description.description ; Beam crossfire correlation degrees**2 between the crossfire laboratory X-axis component and the crossfire laboratory Y-axis component (see <a href="#AXIS">AXIS</a> category). This is a characteristic of the xray 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 directin of each photons in X-Z plane times the deviations of the direction of the same photon in the Y-Z plane around the mean source beam direction. This will be zero for uncorrelated crossfire. Note that some synchrotrons specify this value 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 Pi**2. ; _item.name '<A HREF="#_diffrn_radiation.div_x_y_source">_diffrn_radiation.div_x_y_source</A>' _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_<A name="_diffrn_radiation.filter_edge">_diffrn_radiation.filter_edge</A> _item_description.description ; Absorption edge in angstroms of the radiation filter used. ; _item.name '<A HREF="#_diffrn_radiation.filter_edge">_diffrn_radiation.filter_edge</A>' _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_<A name="_diffrn_radiation.inhomogeneity">_diffrn_radiation.inhomogeneity</A> _item_description.description ; Half-width in millimetres of the incident beam in the direction perpendicular to the diffraction plane. ; _item.name '<A HREF="#_diffrn_radiation.inhomogeneity">_diffrn_radiation.inhomogeneity</A>' _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_<A name="_diffrn_radiation.monochromator">_diffrn_radiation.monochromator</A> _item_description.description ; The method used to obtain monochromatic radiation. If a mono- chromator crystal is used the material and the indices of the Bragg reflection are specified. ; _item.name '<A HREF="#_diffrn_radiation.monochromator">_diffrn_radiation.monochromator</A>' _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_<A name="_diffrn_radiation.polarisn_norm">_diffrn_radiation.polarisn_norm</A> _item_description.description ; The angle in degrees, as viewed from the specimen, between the perpendicular component of the polarisation and the diffraction plane. See _diffrn_radiation_polarisn_ratio. ; _item.name '<A HREF="#_diffrn_radiation.polarisn_norm">_diffrn_radiation.polarisn_norm</A>' _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_<A name="_diffrn_radiation.polarisn_ratio">_diffrn_radiation.polarisn_ratio</A> _item_description.description ; Polarisation ratio of the diffraction beam incident on the crystal. It is the ratio of the perpendicularly polarised to the parallel polarised component of the radiation. The perpendicular component forms an angle of <A HREF="#_diffrn_radiation.polarisn_norm">_diffrn_radiation.polarisn_norm</A> to the normal to the diffraction plane of the sample (i.e. the plane containing the incident and reflected beams). ; _item.name '<A HREF="#_diffrn_radiation.polarisn_ratio">_diffrn_radiation.polarisn_ratio</A>' _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_<A NAME="_diffrn_radiation.polarizn_source_norm">_diffrn_radiation.polarizn_source_norm</A> _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 <a href="#AXIS">AXIS</a> category. Note that this is the angle of polarization of the source photons, either directly from a synchrotron beamline or from a monchromater. This differs from the value of '<A HREF="#_diffrn_radiation.polarisn_norm">_diffrn_radiation.polarisn_norm</A>' in that '<A HREF="#_diffrn_radiation.polarisn_norm">_diffrn_radiation.polarisn_norm</A>' 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 X-Z plane, and the angle as 0. See '_diffrn_radiation.polarizn_source_ratio'. ; _item.name '<A HREF="#_diffrn_radiation.polarizn_source_norm">_diffrn_radiation.polarizn_source_norm</A>' _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_<A NAME="_diffrn_radiation.polarizn_source_ratio">_diffrn_radiation.polarizn_source_ratio</A> _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 plane of the normal to the plane of polarization. Thus, if we had complete polarization in the plane of polarization, the value of '_diffrn_radiation.polarizn_source_ratio' would be 1, and an unpolarized beam 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, for some reason to be, say, perpendicular to the polarization plane (not a common choice), then the Denzo value would be the negative of '_diffrn_radiation.polarizn_source_ratio'. See <A HREF="http://www.hkl-xray.com">http://www.hkl-xray.com</A> for information on Denzo, and Z. Otwinowski and W. Minor, " Processing of X-ray Diffraction Data Collected in Oscillation Mode ", Methods in Enzymology, Volume 276: Macromolecular Crystallography, part A, p.307-326, 1997,C.W. Carter, Jr. & R. M. Sweet, Eds., Academic Press. This differs both in the choice of ratio and choice of orientation from '<A HREF="#_diffrn_radiation.polarisn_ratio">_diffrn_radiation.polarisn_ratio</A>', which, unlike '_diffrn_radiation.polarizn_source_ratio', is unbounded. ; _item.name '<A HREF="#_diffrn_radiation.polarizn_source_ratio">_diffrn_radiation.polarizn_source_ratio</A>' _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_<A name="_diffrn_radiation.probe">_diffrn_radiation.probe</A> _item_description.description ; Name of the type of radiation used. It is strongly encouraged that this field be specified so that the probe radiation can be simply determined. ; _item.name '<A HREF="#_diffrn_radiation.probe">_diffrn_radiation.probe</A>' _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_<A name="_diffrn_radiation.type">_diffrn_radiation.type</A> _item_description.description ; The nature of the radiation. This is typically a description of the X-ray wavelength in Siegbahn notation. ; _item.name '<A HREF="#_diffrn_radiation.type">_diffrn_radiation.type</A>' _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_<A name="_diffrn_radiation.xray_symbol">_diffrn_radiation.xray_symbol</A> _item_description.description ; The IUPAC symbol for the X-ray wavelength for probe radiation. ; _item.name '<A HREF="#_diffrn_radiation.xray_symbol">_diffrn_radiation.xray_symbol</A>' _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_<A name="_diffrn_radiation.wavelength_id">_diffrn_radiation.wavelength_id</A> _item_description.description ; This data item is a pointer to _diffrn_radiation_wavelength.id in the DIFFRN_RADIATION_WAVELENGTH category. ; _item.name '<A HREF="#_diffrn_radiation.wavelength_id">_diffrn_radiation.wavelength_id</A>' _item.mandatory_code yes save_ ################ # <a name="DIFFRN_REFLN">DIFFRN_REFLN</a> # ################ save_DIFFRN_REFLN _category.description ; This category redefinition has been added to extend the key of the standard <a href="#DIFFRN_REFLN">DIFFRN_REFLN</a> category. ; _category.id diffrn_refln _category.mandatory_code no _category_key.name '<a href="#_diffrn_refln.frame_id" >_diffrn_refln.frame_id</a>' loop_ _category_group.id 'inclusive_group' 'diffrn_group' save_ save_<a name="_diffrn_refln.frame_id" >_diffrn_refln.frame_id</a> _item_description.description ; This item is a pointer to <a href="#_diffrn_data_frame.id" >_diffrn_data_frame.id</a> in the <a href="#DIFFRN_DATA_FRAME">DIFFRN_DATA_FRAME</a> category. ; _item.name '<a href="#_diffrn_refln.frame_id" >_diffrn_refln.frame_id</a>' _item.category_id diffrn_refln _item.mandatory_code yes _item_type.code code save_ ############### # <a name="DIFFRN_SCAN">DIFFRN_SCAN</a> # ############### save_DIFFRN_SCAN _category.description ; Data items in the <a href="#DIFFRN_SCAN">DIFFRN_SCAN</a> 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 '<a href="#_diffrn_scan.id" >_diffrn_scan.id</a>' 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 <a href="#AXIS">AXIS</a> category. By making <a href="#_diffrn_scan_axis.scan_id" >_diffrn_scan_axis.scan_id</a> and <a href="#_diffrn_scan_axis.axis_id" >_diffrn_scan_axis.axis_id</a> keys of the <A HREF="#DIFFRN_SCAN_AXIS">DIFFRN_SCAN_AXIS</A> category, an arbitrary number of scanning and fixed axes can be specified for a scan. We have specified three rotation axes and one translation axis at non-zero values, with one axis stepping. There is no reason why more axes could not have been specified to step. We have specified range information, but note that it is redundant from the number of frames and the increment, so we could drop the data item <a href="#_diffrn_scan_axis.angle_range">_diffrn_scan_axis.angle_range</a> . We have specified both the sweep data and the data for a single frame. Note that the information on how the axes are stepped is given twice, once in terms of the overall averages in the value of '<a href="#_diffrn_scan.integration_time" >_diffrn_scan.integration_time</a>' and the values for <a href="#DIFFRN_SCAN_AXIS">DIFFRN_SCAN_AXIS</a>, and precisely for the given frame in the value for '<a href="#_diffrn_scan_frame.integration_time" >_diffrn_scan_frame.integration_time</a>' and the values for <A HREF="#DIFFRN_SCAN_FRAME_AXIS">DIFFRN_SCAN_FRAME_AXIS</A>. If dose-related adjustements are made to scan times and non-linear 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. ; ; <A HREF="#_diffrn_scan.id">_diffrn_scan.id</A> 1 <a href="#_diffrn_scan.date_start" >_diffrn_scan.date_start</a> '2001-11-18T03:26:42' <a href="#_diffrn_scan.date_end" >_diffrn_scan.date_end</a> '2001-11-18T03:36:45' <a href="#_diffrn_scan.integration_time" >_diffrn_scan.integration_time</a> 3.0 <a href="#_diffrn_scan.frame_id_start" >_diffrn_scan.frame_id_start</a> mad_L2_000 <a href="#_diffrn_scan.frame_id_end" >_diffrn_scan.frame_id_end</a> mad_L2_200 <a href="#_diffrn_scan.frames" >_diffrn_scan.frames</a> 201 loop_ <a href="#_diffrn_scan_axis.scan_id" >_diffrn_scan_axis.scan_id</a> <a href="#_diffrn_scan_axis.axis_id" >_diffrn_scan_axis.axis_id</a> <a href="#_diffrn_scan_axis.angle_start" >_diffrn_scan_axis.angle_start</a> <a href="#_diffrn_scan_axis.angle_range" >_diffrn_scan_axis.angle_range</a> <a href="#_diffrn_scan_axis.angle_increment" >_diffrn_scan_axis.angle_increment</a> <a href="#_diffrn_scan_axis.displacement_start" >_diffrn_scan_axis.displacement_start</a> <a href="#_diffrn_scan_axis.displacement_range" >_diffrn_scan_axis.displacement_range</a> <a href="#_diffrn_scan_axis.displacement_increment" >_diffrn_scan_axis.displacement_increment</a> 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 <a href="#_diffrn_scan_frame.scan_id" >_diffrn_scan_frame.scan_id</a> 1 <a href="#_diffrn_scan_frame.date" >_diffrn_scan_frame.date</a> '2001-11-18T03:27:33' <a href="#_diffrn_scan_frame.integration_time" >_diffrn_scan_frame.integration_time</a> 3.0 <a href="#_diffrn_scan_frame.frame_id" >_diffrn_scan_frame.frame_id</a> mad_L2_018 <a href="#_diffrn_scan_frame.frame_number" >_diffrn_scan_frame.frame_number</a> 18 loop_ <a href="#_diffrn_scan_frame_axis.frame_id" >_diffrn_scan_frame_axis.frame_id</a> <a href="#_diffrn_scan_frame_axis.axis_id" >_diffrn_scan_frame_axis.axis_id</a> <A HREF="#_diffrn_scan_frame_axis.angle">_diffrn_scan_frame_axis.angle</A> <a href="#_diffrn_scan_frame_axis.angle_increment" >_diffrn_scan_frame_axis.angle_increment</a> <a href="#_diffrn_scan_frame_axis.displacement" >_diffrn_scan_frame_axis.displacement</a> <a href="#_diffrn_scan_frame_axis.displacement_increment" >_diffrn_scan_frame_axis.displacement_increment</a> 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. Ellis, H. Bernstein. We place a detector 240 mm along the Z axis from the goniometer. This presents us with a choice -- either we define the axes of the detector at the origin, and then put a Z setting of -240 in for the actual use, or we define the axes with the necessary Z-offset. In this case we use the setting, and leave the offset as zero. We call this axis DETECTOR_Z. The axis for positioning the detector in the Y-direction depends on the detector Z-axis. We call this axis, DETECTOR_Y. The axis for positioning the dector in the X-direction depends on the detector Y-axis (and therefore on the detector Z-axis). We call this axis DETECTOR_X. This detector may be rotated around the Y-axis. This rotation axis depends on the three translation axies. We call it DETECTOR_PITCH. We define a coordinate system 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 center 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 <A HREF="#DIFFRN_RADIATION">DIFFRN_RADIATION</A> loop_ <A HREF="#_diffrn_radiation.diffrn_id">_diffrn_radiation.diffrn_id</A> <A HREF="#_diffrn_radiation.wavelength_id">_diffrn_radiation.wavelength_id</A> <A HREF="#_diffrn_radiation.monochromator">_diffrn_radiation.monochromator</A> <A HREF="#_diffrn_radiation.polarizn_source_ratio">_diffrn_radiation.polarizn_source_ratio</A> <A HREF="#_diffrn_radiation.polarizn_source_norm">_diffrn_radiation.polarizn_source_norm</A> <A HREF="#_diffrn_radiation.div_x_source">_diffrn_radiation.div_x_source</A> <A HREF="#_diffrn_radiation.div_y_source">_diffrn_radiation.div_y_source</A> <A HREF="#_diffrn_radiation.div_x_y_source">_diffrn_radiation.div_x_y_source</A> 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 <A HREF="#DIFFRN_DETECTOR">DIFFRN_DETECTOR</A> loop_ <A HREF="#_diffrn_detector.diffrn_id">_diffrn_detector.diffrn_id</A> <A HREF="#_diffrn_detector.id">_diffrn_detector.id</A> <A HREF="#_diffrn_detector.type">_diffrn_detector.type</A> <A HREF="#_diffrn_detector.number_of_axes">_diffrn_detector.number_of_axes</A> P6MB MAR345-SN26 'MAR 345' 4 # category <a href="#DIFFRN_DETECTOR_AXIS">DIFFRN_DETECTOR_AXIS</a> loop_ <A HREF="#_diffrn_detector_axis.id">_diffrn_detector_axis.id</A> <A HREF="#_diffrn_detector_axis.axis_id">_diffrn_detector_axis.axis_id</A> MAR345-SN26 DETECTOR_X MAR345-SN26 DETECTOR_Y MAR345-SN26 DETECTOR_Z MAR345-SN26 DETECTOR_PITCH # category <a href="#DIFFRN_DETECTOR_ELEMENT">DIFFRN_DETECTOR_ELEMENT</a> loop_ <A HREF="#_diffrn_detector_element.id">_diffrn_detector_element.id</A> <A HREF="_diffrn_detector_element.detector_id#">_diffrn_detector_element.detector_id</A> ELEMENT1 MAR345-SN26 # category <a href="#DIFFRN_DATA_FRAME">DIFFRN_DATA_FRAME</a> loop_ <A HREF="#_diffrn_data_frame.id">_diffrn_data_frame.id</A> <A HREF="#_diffrn_data_frame.detector_element_id">_diffrn_data_frame.detector_element_id</A> <A HREF="#_diffrn_data_frame.array_id">_diffrn_data_frame.array_id</A> <A HREF="#_diffrn_data_frame.binary_id">_diffrn_data_frame.binary_id</A> FRAME1 ELEMENT1 ARRAY1 1 # category <a href="#DIFFRN_MEASUREMENT">DIFFRN_MEASUREMENT</a> loop_ <A HREF="#_diffrn_measurement.diffrn_id">_diffrn_measurement.diffrn_id</A> <A HREF="#_diffrn_measurement.id">_diffrn_measurement.id</A> <A HREF="#_diffrn_measurement.number_of_axes">_diffrn_measurement.number_of_axes</A> <A HREF="#_diffrn_measurement.method">_diffrn_measurement.method</A> P6MB GONIOMETER 3 rotation # category <a href="#DIFFRN_MEASUREMENT_AXIS">DIFFRN_MEASUREMENT_AXIS</a> loop_ <A HREF="#_diffrn_measurement_axis.measurement_id">_diffrn_measurement_axis.measurement_id</A> <A HREF="#_diffrn_measurement_axis.axis_id">_diffrn_measurement_axis.axis_id</A> GONIOMETER GONIOMETER_PHI GONIOMETER GONIOMETER_KAPPA GONIOMETER GONIOMETER_OMEGA # category <a href="#DIFFRN_SCAN">DIFFRN_SCAN</a> loop_ <a href="#_diffrn_scan.id" >_diffrn_scan.id</a> <a href="#_diffrn_scan.frame_id_start" >_diffrn_scan.frame_id_start</a> <a href="#_diffrn_scan.frame_id_end" >_diffrn_scan.frame_id_end</a> <a href="#_diffrn_scan.frames" >_diffrn_scan.frames</a> SCAN1 FRAME1 FRAME1 1 # category <a href="#DIFFRN_SCAN_AXIS">DIFFRN_SCAN_AXIS</a> loop_ <a href="#_diffrn_scan_axis.scan_id" >_diffrn_scan_axis.scan_id</a> <a href="#_diffrn_scan_axis.axis_id" >_diffrn_scan_axis.axis_id</a> <a href="#_diffrn_scan_axis.angle_start" >_diffrn_scan_axis.angle_start</a> <a href="#_diffrn_scan_axis.angle_range" >_diffrn_scan_axis.angle_range</a> <a href="#_diffrn_scan_axis.angle_increment" >_diffrn_scan_axis.angle_increment</a> <a href="#_diffrn_scan_axis.displacement_start" >_diffrn_scan_axis.displacement_start</a> <a href="#_diffrn_scan_axis.displacement_range" >_diffrn_scan_axis.displacement_range</a> <a href="#_diffrn_scan_axis.displacement_increment" >_diffrn_scan_axis.displacement_increment</a> 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 <a href="#DIFFRN_SCAN_FRAME">DIFFRN_SCAN_FRAME</a> loop_ <a href="#_diffrn_scan_frame.frame_id" >_diffrn_scan_frame.frame_id</a> <a href="#_diffrn_scan_frame.frame_number" >_diffrn_scan_frame.frame_number</a> <a href="#_diffrn_scan_frame.integration_time" >_diffrn_scan_frame.integration_time</a> <a href="#_diffrn_scan_frame.scan_id" >_diffrn_scan_frame.scan_id</a> <a href="#_diffrn_scan_frame.date" >_diffrn_scan_frame.date</a> FRAME1 1 20.0 SCAN1 1997-12-04T10:23:48 # category <a href="#DIFFRN_SCAN_FRAME_AXIS">DIFFRN_SCAN_FRAME_AXIS</a> loop_ <a href="#_diffrn_scan_frame_axis.frame_id" >_diffrn_scan_frame_axis.frame_id</a> <a href="#_diffrn_scan_frame_axis.axis_id" >_diffrn_scan_frame_axis.axis_id</a> <a href="#_diffrn_scan_frame_axis.angle" >_diffrn_scan_frame_axis.angle</a> <a href="#_diffrn_scan_frame_axis.displacement" >_diffrn_scan_frame_axis.displacement</a> FRAME1 GONIOMETER_OMEGA 12.0 0.0 FRAME1 GONIOMETER_KAPPA 23.3 0.0 FRAME1 GONIOMETER_PHI -165.8 0.0 FRAME1 DETECTOR_Z 0.0 -240.0 FRAME1 DETECTOR_Y 0.0 0.6 FRAME1 DETECTOR_X 0.0 -0.5 FRAME1 DETECTOR_PITCH 0.0 0.0 # category <a href="#AXIS">AXIS</a> loop_ <A HREF="#_axis.id">_axis.id</A> <A HREF="#_axis.type">_axis.type</A> <A HREF="#_axis.equipment">_axis.equipment</A> <A HREF="#_axis.depends_on">_axis.depends_on</A> <A HREF="#_axis.vector[1]">_axis.vector[1]</A> <A HREF="#_axis.vector[2]">_axis.vector[2]</A> <A HREF="#_axis.vector[3]">_axis.vector[3]</A> <A HREF="#_axis.offset[1]">_axis.offset[1]</A> <A HREF="#_axis.offset[2]">_axis.offset[2]</A> <A HREF="#_axis.offset[3]">_axis.offset[3]</A> GONIOMETER_OMEGA rotation goniometer . 1 0 0 . . . GONIOMETER_KAPPA rotation goniometer GONIOMETER_OMEGA 0.64279 0 0.76604 . . . GONIOMETER_PHI rotation goniometer GONIOMETER_KAPPA 1 0 0 . . . SOURCE general source . 0 0 1 . . . GRAVITY general gravity . 0 -1 0 . . . DETECTOR_Z translation detector . 0 0 1 0 0 0 DETECTOR_Y translation detector DETECTOR_Z 0 1 0 0 0 0 DETECTOR_X translation detector DETECTOR_Y 1 0 0 0 0 0 DETECTOR_PITCH rotation detector DETECTOR_X 0 1 0 0 0 0 ELEMENT_X translation detector DETECTOR_PITCH 1 0 0 172.43 -172.43 0 ELEMENT_Y translation detector ELEMENT_X 0 1 0 0 0 0 # category <a href="#ARRAY_STRUCTURE_LIST">ARRAY_STRUCTURE_LIST</a> loop_ <A HREF="#_array_structure_list.array_id">_array_structure_list.array_id</A> <A HREF="#_array_structure_list.index">_array_structure_list.index</A> <A HREF="#_array_structure_list.dimension">_array_structure_list.dimension</A> <A HREF="#_array_structure_list.precedence">_array_structure_list.precedence</A> <A HREF="#_array_structure_list.direction">_array_structure_list.direction</A> <A HREF="#_array_structure_list.axis_set_id">_array_structure_list.axis_set_id</A> ARRAY1 1 2300 1 increasing ELEMENT_X ARRAY1 2 2300 2 increasing ELEMENT_Y # category <a href="#ARRAY_STRUCTURE_LIST_AXIS">ARRAY_STRUCTURE_LIST_AXIS</a> loop_ <A HREF="#_array_structure_list_axis.axis_set_id">_array_structure_list_axis.axis_set_id</A> <A HREF="#_array_structure_list_axis.axis_id">_array_structure_list_axis.axis_id</A> <A HREF="#_array_structure_list_axis.displacement">_array_structure_list_axis.displacement</A> <A HREF="#_array_structure_list_axis.displacement_increment">_array_structure_list_axis.displacement_increment</A> ELEMENT_X ELEMENT_X 0.075 0.150 ELEMENT_Y ELEMENT_Y 0.075 0.150 # category <a href="#ARRAY_ELEMENT_SIZE">ARRAY_ELEMENT_SIZE</a> loop_ <A HREF="#_array_element_size.array_id">_array_element_size.array_id</A> <A HREF="#_array_element_size.index">_array_element_size.index</A> <A HREF="#_array_element_size.index">_array_element_size.size</A> ARRAY1 1 150e-6 ARRAY1 2 150e-6 # category <a href="#ARRAY_INTENSITIES">ARRAY_INTENSITIES</a> loop_ <A HREF="#_array_intensities.array_id">_array_intensities.array_id</A> <A HREF="#_array_intensities.binary_id">_array_intensities.binary_id</A> <A HREF="#_array_intensities.linearity">_array_intensities.linearity</A> <A HREF="#_array_intensities.gain">_array_intensities.gain</A> <A HREF="#_array_intensities.gain_esd">_array_intensities.gain_esd</A> <A HREF="#_array_intensities.overload">_array_intensities.overload</A> <A HREF="#_array_intensities.undefined_value">_array_intensities.undefined_value</A> ARRAY1 1 linear 1.15 0.2 240000 0 # category <a href="#ARRAY_STRUCTURE">ARRAY_STRUCTURE</a> loop_ <A HREF="#_array_structure.id">_array_structure.id</A> <A HREF="#_array_structure.encoding_type">_array_structure.encoding_type</A> <A HREF="#_array_structure.compression_type">_array_structure.compression_type</A> <A HREF="#_array_structure.byte_order">_array_structure.byte_order</A> ARRAY1 "signed 32-bit integer" packed little_endian # category <a href="#ARRAY_DATA">ARRAY_DATA</a> loop_ <A HREF="#_array_data.array_id">_array_data.array_id</A> <A HREF="#_array_data.binary_id">_array_data.binary_id</A> <A HREF="#_array_data.data">_array_data.data</A> ARRAY1 1 ; --CIF-BINARY-FORMAT-SECTION-- Content-Type: application/octet-stream; conversions="x-CBF_PACKED" Content-Transfer-Encoding: BASE64 X-Binary-Size: 3801324 X-Binary-ID: 1 X-Binary-Element-Type: "signed 32-bit integer" Content-MD5: 07lZFvF+aOcW85IN7usl8A== AABRAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAZBQSr1sKNBOeOe9HITdMdDUnbq7bg ... 8REo6TtBrxJ1vKqAvx9YDMD6J18Qg83OMr/tgssjMIJMXATDsZobL90AEXc4KigE --CIF-BINARY-FORMAT-SECTION---- ; ; ; Example 3 - Example 2 revised for a spiral scan, R. M. Sweet, P. Ellis, H. Bernstein. We place a detector 240 mm along the Z axis from the goniometer, as in Example 2, above, but in this example, the image plate is scanned in a spiral pattern outside edge in. The axis for positioning the detector in the Y-direction depends on the detector Z-axis. We call this axis, DETECTOR_Y. The axis for positioning the dector in the X-direction depends on the detector Y-axis (and therefore on the detector Z-axis). We call this axis DETECTOR_X. This detector may be rotated around the Y-axis. This rotation axis depends on the three translation axies. We call it DETECTOR_PITCH. We define a coordinate system on the face of the detector in terms of a coupled rotation axis and radial scan axis to form a spiral scan. Let us call rotation axis ELEMENT_ROT, and the radial axis ELEMENT_RAD. We assume 150 um radial pitch and 75 um 'constant velocity' angular pitch. We index first on the rotation axis and make the radial axis dependent on it. The two axes are coupled to form an axis set ELEMENT_SPIRAL. ; ; ###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 <A HREF="#DIFFRN_RADIATION">DIFFRN_RADIATION</A> loop_ <A HREF="#_diffrn_radiation.diffrn_id">_diffrn_radiation.diffrn_id</A> <A HREF="#_diffrn_radiation.wavelength_id">_diffrn_radiation.wavelength_id</A> <A HREF="#_diffrn_radiation.monochromator">_diffrn_radiation.monochromator</A> <A HREF="#_diffrn_radiation.polarizn_source_ratio">_diffrn_radiation.polarizn_source_ratio</A> <A HREF="#_diffrn_radiation.polarizn_source_norm">_diffrn_radiation.polarizn_source_norm</A> <A HREF="#_diffrn_radiation.div_x_source">_diffrn_radiation.div_x_source</A> <A HREF="#_diffrn_radiation.div_y_source">_diffrn_radiation.div_y_source</A> <A HREF="#_diffrn_radiation.div_x_y_source">_diffrn_radiation.div_x_y_source</A> 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 <A HREF="#DIFFRN_DETECTOR">DIFFRN_DETECTOR</A> loop_ <A HREF="#_diffrn_detector.diffrn_id">_diffrn_detector.diffrn_id</A> <A HREF="#_diffrn_detector.id">_diffrn_detector.id</A> <A HREF="#_diffrn_detector.type">_diffrn_detector.type</A> <A HREF="#_diffrn_detector.number_of_axes">_diffrn_detector.number_of_axes</A> P6MB MAR345-SN26 'MAR 345' 4 # category <a href="#DIFFRN_DETECTOR_AXIS">DIFFRN_DETECTOR_AXIS</a> loop_ <A HREF="#_diffrn_detector_axis.id">_diffrn_detector_axis.id</A> <A HREF="#_diffrn_detector_axis.axis_id">_diffrn_detector_axis.axis_id</A> MAR345-SN26 DETECTOR_X MAR345-SN26 DETECTOR_Y MAR345-SN26 DETECTOR_Z MAR345-SN26 DETECTOR_PITCH # category <a href="#DIFFRN_DETECTOR_ELEMENT">DIFFRN_DETECTOR_ELEMENT</a> loop_ <A HREF="#_diffrn_detector_element.id">_diffrn_detector_element.id</A> <A HREF="_diffrn_detector_element.detector_id#">_diffrn_detector_element.detector_id</A> ELEMENT1 MAR345-SN26 # category <a href="#DIFFRN_DATA_FRAME">DIFFRN_DATA_FRAME</a> loop_ <A HREF="#_diffrn_data_frame.id">_diffrn_data_frame.id</A> <A HREF="#_diffrn_data_frame.detector_element_id">_diffrn_data_frame.detector_element_id</A> <A HREF="#_diffrn_data_frame.array_id">_diffrn_data_frame.array_id</A> <A HREF="#_diffrn_data_frame.binary_id">_diffrn_data_frame.binary_id</A> FRAME1 ELEMENT1 ARRAY1 1 # category <a href="#DIFFRN_MEASUREMENT">DIFFRN_MEASUREMENT</a> loop_ <A HREF="#_diffrn_measurement.diffrn_id">_diffrn_measurement.diffrn_id</A> <A HREF="#_diffrn_measurement.id">_diffrn_measurement.id</A> <A HREF="#_diffrn_measurement.number_of_axes">_diffrn_measurement.number_of_axes</A> <A HREF="#_diffrn_measurement.method">_diffrn_measurement.method</A> P6MB GONIOMETER 3 rotation # category <a href="#DIFFRN_MEASUREMENT_AXIS">DIFFRN_MEASUREMENT_AXIS</a> loop_ <A HREF="#_diffrn_measurement_axis.measurement_id">_diffrn_measurement_axis.measurement_id</A> <A HREF="#_diffrn_measurement_axis.axis_id">_diffrn_measurement_axis.axis_id</A> GONIOMETER GONIOMETER_PHI GONIOMETER GONIOMETER_KAPPA GONIOMETER GONIOMETER_OMEGA # category <a href="#DIFFRN_SCAN">DIFFRN_SCAN</a> loop_ <a href="#_diffrn_scan.id" >_diffrn_scan.id</a> <a href="#_diffrn_scan.frame_id_start" >_diffrn_scan.frame_id_start</a> <a href="#_diffrn_scan.frame_id_end" >_diffrn_scan.frame_id_end</a> <a href="#_diffrn_scan.frames" >_diffrn_scan.frames</a> SCAN1 FRAME1 FRAME1 1 # category <a href="#DIFFRN_SCAN_AXIS">DIFFRN_SCAN_AXIS</a> loop_ <a href="#_diffrn_scan_axis.scan_id" >_diffrn_scan_axis.scan_id</a> <a href="#_diffrn_scan_axis.axis_id" >_diffrn_scan_axis.axis_id</a> <a href="#_diffrn_scan_axis.angle_start" >_diffrn_scan_axis.angle_start</a> <a href="#_diffrn_scan_axis.angle_range" >_diffrn_scan_axis.angle_range</a> <a href="#_diffrn_scan_axis.angle_increment" >_diffrn_scan_axis.angle_increment</a> <a href="#_diffrn_scan_axis.displacement_start" >_diffrn_scan_axis.displacement_start</a> <a href="#_diffrn_scan_axis.displacement_range" >_diffrn_scan_axis.displacement_range</a> <a href="#_diffrn_scan_axis.displacement_increment" >_diffrn_scan_axis.displacement_increment</a> 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 <a href="#DIFFRN_SCAN_FRAME">DIFFRN_SCAN_FRAME</a> loop_ <a href="#_diffrn_scan_frame.frame_id" >_diffrn_scan_frame.frame_id</a> <a href="#_diffrn_scan_frame.frame_number" >_diffrn_scan_frame.frame_number</a> <a href="#_diffrn_scan_frame.integration_time" >_diffrn_scan_frame.integration_time</a> <a href="#_diffrn_scan_frame.scan_id" >_diffrn_scan_frame.scan_id</a> <a href="#_diffrn_scan_frame.date" >_diffrn_scan_frame.date</a> FRAME1 1 20.0 SCAN1 1997-12-04T10:23:48 # category <a href="#DIFFRN_SCAN_FRAME_AXIS">DIFFRN_SCAN_FRAME_AXIS</a> loop_ <a href="#_diffrn_scan_frame_axis.frame_id" >_diffrn_scan_frame_axis.frame_id</a> <a href="#_diffrn_scan_frame_axis.axis_id" >_diffrn_scan_frame_axis.axis_id</a> <a href="#_diffrn_scan_frame_axis.angle" >_diffrn_scan_frame_axis.angle</a> <a href="#_diffrn_scan_frame_axis.displacement" >_diffrn_scan_frame_axis.displacement</a> FRAME1 GONIOMETER_OMEGA 12.0 0.0 FRAME1 GONIOMETER_KAPPA 23.3 0.0 FRAME1 GONIOMETER_PHI -165.8 0.0 FRAME1 DETECTOR_Z 0.0 -240.0 FRAME1 DETECTOR_Y 0.0 0.6 FRAME1 DETECTOR_X 0.0 -0.5 FRAME1 DETECTOR_PITCH 0.0 0.0 # category <a href="#AXIS">AXIS</a> loop_ <A HREF="#_axis.id">_axis.id</A> <A HREF="#_axis.type">_axis.type</A> <A HREF="#_axis.equipment">_axis.equipment</A> <A HREF="#_axis.depends_on">_axis.depends_on</A> <A HREF="#_axis.vector[1]">_axis.vector[1]</A> <A HREF="#_axis.vector[2]">_axis.vector[2]</A> <A HREF="#_axis.vector[3]">_axis.vector[3]</A> <A HREF="#_axis.offset[1]">_axis.offset[1]</A> <A HREF="#_axis.offset[2]">_axis.offset[2]</A> <A HREF="#_axis.offset[3]">_axis.offset[3]</A> GONIOMETER_OMEGA rotation goniometer . 1 0 0 . . . GONIOMETER_KAPPA rotation goniometer GONIOMETER_OMEGA 0.64279 0 0.76604 . . . GONIOMETER_PHI rotation goniometer GONIOMETER_KAPPA 1 0 0 . . . SOURCE general source . 0 0 1 . . . GRAVITY general gravity . 0 -1 0 . . . DETECTOR_Z translation detector . 0 0 1 0 0 0 DETECTOR_Y translation detector DETECTOR_Z 0 1 0 0 0 0 DETECTOR_X translation detector DETECTOR_Y 1 0 0 0 0 0 DETECTOR_PITCH rotation detector DETECTOR_X 0 1 0 0 0 0 ELEMENT_ROT translation detector DETECTOR_PITCH 0 0 1 0 0 0 ELEMENT_RAD translation detector ELEMENT_ROT 0 1 0 0 0 0 # category <a href="#ARRAY_STRUCTURE_LIST">ARRAY_STRUCTURE_LIST</a> loop_ <A HREF="#_array_structure_list.array_id">_array_structure_list.array_id</A> <A HREF="#_array_structure_list.index">_array_structure_list.index</A> <A HREF="#_array_structure_list.dimension">_array_structure_list.dimension</A> <A HREF="#_array_structure_list.precedence">_array_structure_list.precedence</A> <A HREF="#_array_structure_list.direction">_array_structure_list.direction</A> <A HREF="#_array_structure_list.axis_set_id">_array_structure_list.axis_set_id</A> ARRAY1 1 8309900 1 increasing ELEMENT_SPIRAL # category <a href="#ARRAY_STRUCTURE_LIST_AXIS">ARRAY_STRUCTURE_LIST_AXIS</a> loop_ <A HREF="#_array_structure_list_axis.axis_set_id">_array_structure_list_axis.axis_set_id</A> <A HREF="#_array_structure_list_axis.axis_id">_array_structure_list_axis.axis_id</A> <A HREF="#_array_structure_list_axis.angle">_array_structure_list_axis.angle</A> <A HREF="#_array_structure_list_axis.displacement">_array_structure_list_axis.displacement</A> <A HREF="#_array_structure_list_axis.angular_pitch">_array_structure_list_axis.angular_pitch</A> <A HREF="#_array_structure_list_axis.radial_pitch">_array_structure_list_axis.radial_pitch</A> ELEMENT_SPIRAL ELEMENT_ROT 0 . 0.075 . ELEMENT_SPIRAL ELEMENT_RAD . 172.5 . -0.150 # category <a href="#ARRAY_ELEMENT_SIZE">ARRAY_ELEMENT_SIZE</a> # the actual pixels are 0.075 by 0.150 mm # We give the coarser dimension here. loop_ <A HREF="#_array_element_size.array_id">_array_element_size.array_id</A> <A HREF="#_array_element_size.index">_array_element_size.index</A> <A HREF="#_array_element_size.index">_array_element_size.size</A> ARRAY1 1 150e-6 # category <a href="#ARRAY_INTENSITIES">ARRAY_INTENSITIES</a> loop_ <A HREF="#_array_intensities.array_id">_array_intensities.array_id</A> <A HREF="#_array_intensities.binary_id">_array_intensities.binary_id</A> <A HREF="#_array_intensities.linearity">_array_intensities.linearity</A> <A HREF="#_array_intensities.gain">_array_intensities.gain</A> <A HREF="#_array_intensities.gain_esd">_array_intensities.gain_esd</A> <A HREF="#_array_intensities.overload">_array_intensities.overload</A> <A HREF="#_array_intensities.undefined_value">_array_intensities.undefined_value</A> ARRAY1 1 linear 1.15 0.2 240000 0 # category <a href="#ARRAY_STRUCTURE">ARRAY_STRUCTURE</a> loop_ <A HREF="#_array_structure.id">_array_structure.id</A> <A HREF="#_array_structure.encoding_type">_array_structure.encoding_type</A> <A HREF="#_array_structure.compression_type">_array_structure.compression_type</A> <A HREF="#_array_structure.byte_order">_array_structure.byte_order</A> ARRAY1 "signed 32-bit integer" packed little_endian # category <a href="#ARRAY_DATA">ARRAY_DATA</a> loop_ <A HREF="#_array_data.array_id">_array_data.array_id</A> <A HREF="#_array_data.binary_id">_array_data.binary_id</A> <A HREF="#_array_data.data">_array_data.data</A> ARRAY1 1 ; --CIF-BINARY-FORMAT-SECTION-- Content-Type: application/octet-stream; conversions="x-CBF_PACKED" Content-Transfer-Encoding: BASE64 X-Binary-Size: 3801324 X-Binary-ID: 1 X-Binary-Element-Type: "signed 32-bit integer" Content-MD5: 07lZFvF+aOcW85IN7usl8A== AABRAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAZBQSr1sKNBOeOe9HITdMdDUnbq7bg ... 8REo6TtBrxJ1vKqAvx9YDMD6J18Qg83OMr/tgssjMIJMXATDsZobL90AEXc4KigE --CIF-BINARY-FORMAT-SECTION---- ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save_<a name="_diffrn_scan.id" >_diffrn_scan.id</a> _item_description.description ; The value of <a href="#_diffrn_scan.id" >_diffrn_scan.id</a> uniquely identifies each scan. The identifier is used to tie together all the information about the scan. ; loop_ _item.name _item.category_id _item.mandatory_code '<a href="#_diffrn_scan.id" >_diffrn_scan.id</a>' diffrn_scan yes '<a href="#_diffrn_scan_axis.scan_id" >_diffrn_scan_axis.scan_id</a>' diffrn_scan_axis yes '<a href="#_diffrn_scan_frame.scan_id" >_diffrn_scan_frame.scan_id</a>' diffrn_scan_frame yes _item_type.code code loop_ _item_linked.child_name _item_linked.parent_name '<a href="#_diffrn_scan_axis.scan_id" >_diffrn_scan_axis.scan_id</a>' '<a href="#_diffrn_scan.id" >_diffrn_scan.id</a>' '<a href="#_diffrn_scan_frame.scan_id" >_diffrn_scan_frame.scan_id</a>' '<a href="#_diffrn_scan.id" >_diffrn_scan.id</a>' save_ save_<A NAME="_diffrn_scan.date_end">_diffrn_scan.date_end</A> _item_description.description ; The date and time of the end of the scan. Note that this may be an estimate generated during the scan, before the precise time of the end of the scan is known. ; _item.name '<A HREF="#_diffrn_scan.date_end">_diffrn_scan.date_end</A>' _item.category_id diffrn_scan _item.mandatory_code no _item_type.code yyyy-mm-dd save_ save_<A NAME="_diffrn_scan.date_start">_diffrn_scan.date_start</A> _item_description.description ; The date and time of the start of the scan. ; _item.name '<A HREF="#_diffrn_scan.date_start">_diffrn_scan.date_start</A>' _item.category_id diffrn_scan _item.mandatory_code no _item_type.code yyyy-mm-dd save_ save_<a name="_diffrn_scan.integration_time" >_diffrn_scan.integration_time</a> _item_description.description ; Approximate average time in seconds to integrate each step of the scan. The precise time for integration of each particular step must be provided in '<a href="#_diffrn_scan_frame.integration_time" >_diffrn_scan_frame.integration_time</a>', even if all steps have the same integration time. ; _item.name '<a href="#_diffrn_scan.integration_time" >_diffrn_scan.integration_time</a>' _item.category_id diffrn_scan _item.mandatory_code no _item_type.code float _item_units.code 'seconds' loop_ _item_range.maximum _item_range.minimum . 0.0 save_ save_<a name="_diffrn_scan.frame_id_start" >_diffrn_scan.frame_id_start</a> _item_description.description ; The value of this data item is the identifier of the first frame in the scan. This item is a pointer to <a href="#_diffrn_data_frame.id" >_diffrn_data_frame.id</a> in the <a href="#DIFFRN_DATA_FRAME">DIFFRN_DATA_FRAME</a> category. ; _item.name '<a href="#_diffrn_scan.frame_id_start" >_diffrn_scan.frame_id_start</a>' _item.category_id diffrn_scan _item.mandatory_code yes save_ save_<a name="_diffrn_scan.frame_id_end" >_diffrn_scan.frame_id_end</a> _item_description.description ; The value of this data item is the identifier of the last frame in the scan. This item is a pointer to <a href="#_diffrn_data_frame.id" >_diffrn_data_frame.id</a> in the <a href="#DIFFRN_DATA_FRAME">DIFFRN_DATA_FRAME</a> category. ; _item.name '<a href="#_diffrn_scan.frame_id_end" >_diffrn_scan.frame_id_end</a>' _item.category_id diffrn_scan _item.mandatory_code yes save_ save_<a name="_diffrn_scan.frames" >_diffrn_scan.frames</a> _item_description.description ; The value of this data item is the number of frames in the scan. ; _item.name '<a href="#_diffrn_scan.frames" >_diffrn_scan.frames</a>' _item.category_id diffrn_scan _item.mandatory_code no _item_type.code int loop_ _item_range.maximum _item_range.minimum . 1 1 1 save_ #################### # <a name="DIFFRN_SCAN_AXIS">DIFFRN_SCAN_AXIS</a> # #################### save_DIFFRN_SCAN_AXIS _category.description ; Data items in the <a href="#DIFFRN_SCAN_AXIS">DIFFRN_SCAN_AXIS</a> category describe the settings of axes for particular scans. Unspecified axes are assumed to be at their zero points. ; _category.id diffrn_scan_axis _category.mandatory_code no loop_ _category_key.name '<a href="#_diffrn_scan_axis.scan_id" >_diffrn_scan_axis.scan_id</a>' '<a href="#_diffrn_scan_axis.axis_id" >_diffrn_scan_axis.axis_id</a>' loop_ _category_group.id 'inclusive_group' 'diffrn_group' save_ save_<a name="_diffrn_scan_axis.scan_id" >_diffrn_scan_axis.scan_id</a> _item_description.description ; The value of this data item is the identifier of the scan for which axis settings are being specified. Multiple axes may be specified for the same value of '<a href="#_diffrn_scan.id" >_diffrn_scan.id</a>'. This item is a pointer to <a href="#_diffrn_scan.id" >_diffrn_scan.id</a> in the <a href="#DIFFRN_SCAN">DIFFRN_SCAN</a> category. ; _item.name '<a href="#_diffrn_scan_axis.scan_id" >_diffrn_scan_axis.scan_id</a>' _item.category_id diffrn_scan_axis _item.mandatory_code yes save_ save_<a name="_diffrn_scan_axis.axis_id" >_diffrn_scan_axis.axis_id</a> _item_description.description ; The value of this data item is the identifier of one of the axes for the scan for which settings are being specified. Multiple axes may be specified for the same value of '<a href="#_diffrn_scan.id" >_diffrn_scan.id</a>'. This item is a pointer to <a href="#_axis.id" >_axis.id</a> in the AXIS category. ; _item.name '<a href="#_diffrn_scan_axis.axis_id" >_diffrn_scan_axis.axis_id</a>' _item.category_id diffrn_scan_axis _item.mandatory_code yes save_ save_<a name="_diffrn_scan_axis.angle_start" >_diffrn_scan_axis.angle_start</a> _item_description.description ; The starting position for the specified axis in degrees. ; _item.name '<a href="#_diffrn_scan_axis.angle_start" >_diffrn_scan_axis.angle_start</a>' _item.category_id diffrn_scan_axis _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'degrees' save_ save_<a name="_diffrn_scan_axis.angle_range" >_diffrn_scan_axis.angle_range</a> _item_description.description ; The range from the starting position for the specified axis in degrees. ; _item.name '<a href="#_diffrn_scan_axis.angle_range" >_diffrn_scan_axis.angle_range</a>' _item.category_id diffrn_scan_axis _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'degrees' save_ save_<a name="_diffrn_scan_axis.angle_increment" >_diffrn_scan_axis.angle_increment</a> _item_description.description ; The increment for each step for the specified axis in degrees. In general, this will agree with '<a href="#_diffrn_scan_frame_axis.angle_increment" >_diffrn_scan_frame_axis.angle_increment</a>', which see for a precise description. ; _item.name '<a href="#_diffrn_scan_axis.angle_increment" >_diffrn_scan_axis.angle_increment</a>' _item.category_id diffrn_scan_axis _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'degrees' save_ save_<A NAME="_diffrn_scan_axis.angle_rstrt_incr">_diffrn_scan_axis.angle_rstrt_incr</A> _item_description.description ; The increment after each step for the specified axis in degrees. In general, this will agree with '<a href="#_diffrn_scan_frame_axis.angle_increment" >_diffrn_scan_frame_axis.angle_increment</a>', which see for a precise description. ; _item.name '<A HREF="#_diffrn_scan_axis.angle_rstrt_incr">_diffrn_scan_axis.angle_rstrt_incr</A>' _item.category_id diffrn_scan_axis _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'degrees' save_ save_<a name="_diffrn_scan_axis.displacement_start" >_diffrn_scan_axis.displacement_start</a> _item_description.description ; The starting position for the specified axis in millimetres. ; _item.name '<a href="#_diffrn_scan_axis.displacement_start" >_diffrn_scan_axis.displacement_start</a>' _item.category_id diffrn_scan_axis _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'millimetres' save_ save_<a name="_diffrn_scan_axis.displacement_range" >_diffrn_scan_axis.displacement_range</a> _item_description.description ; The range from the starting position for the specified axis in millimetres. ; _item.name '<a href="#_diffrn_scan_axis.displacement_range" >_diffrn_scan_axis.displacement_range</a>' _item.category_id diffrn_scan_axis _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'millimetres' save_ save_<a name="_diffrn_scan_axis.displacement_increment" >_diffrn_scan_axis.displacement_increment</a> _item_description.description ; The increment for each step for the specified axis in millimetres. In general, this will agree with '<A HREF="#_diffrn_scan_frame_axis.displacement_increment">_diffrn_scan_frame_axis.displacement_increment</A>', which see for a precise description. ; _item.name '<a href="#_diffrn_scan_axis.displacement_increment" >_diffrn_scan_axis.displacement_increment</a>' _item.category_id diffrn_scan_axis _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'millimetres' save_ save_<A NAME="_diffrn_scan_axis.displacement_rstrt_incr">_diffrn_scan_axis.displacement_rstrt_incr</A> _item_description.description ; The increment for each step for the specified axis in millimetres. In general, this will agree with '<A HREF="#_diffrn_scan_frame_axis.displacement_rstrt_incr">_diffrn_scan_frame_axis.displacement_rstrt_incr</A>', which see for a precise description. ; _item.name '<A HREF="#_diffrn_scan_axis.displacement_rstrt_incr">_diffrn_scan_axis.displacement_rstrt_incr</A>' _item.category_id diffrn_scan_axis _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'millimetres' save_ ##################### # <a name="DIFFRN_SCAN_FRAME">DIFFRN_SCAN_FRAME</a> # ##################### save_DIFFRN_SCAN_FRAME _category.description ; Data items in the <a href="#DIFFRN_SCAN_FRAME">DIFFRN_SCAN_FRAME</a> category describe the relationship of particular frames to scans. ; _category.id diffrn_scan_frame _category.mandatory_code no loop_ _category_key.name '<a href="#_diffrn_scan_frame.scan_id" >_diffrn_scan_frame.scan_id</a>' '<a href="#_diffrn_scan_frame.frame_id" >_diffrn_scan_frame.frame_id</a>' loop_ _category_group.id 'inclusive_group' 'diffrn_group' save_ save_<A NAME="_diffrn_scan_frame.date">_diffrn_scan_frame.date</A> _item_description.description ; The date and time of the start of the frame being scanned. ; _item.name '<A HREF="#_diffrn_scan_frame.date">_diffrn_scan_frame.date</A>' _item.category_id diffrn_scan_frame _item.mandatory_code no _item_type.code yyyy-mm-dd save_ save_<a name="_diffrn_scan_frame.frame_id" >_diffrn_scan_frame.frame_id</a> _item_description.description ; The value of this data item is the identifier of the frame being examined. This item is a pointer to <a href="#_diffrn_data_frame.id" >_diffrn_data_frame.id</a> in the <a href="#DIFFRN_DATA_FRAME">DIFFRN_DATA_FRAME</a> category. ; _item.name '<a href="#_diffrn_scan_frame.frame_id" >_diffrn_scan_frame.frame_id</a>' _item.category_id diffrn_scan_frame _item.mandatory_code yes save_ save_<a name="_diffrn_scan_frame.frame_number" >_diffrn_scan_frame.frame_number</a> _item_description.description ; The value of this data item is the number of the frame within the scan, starting with 1. It is not necessarily the same as the value of <a href="#_diffrn_scan_frame.frame_id">_diffrn_scan_frame.frame_id</a>, but may be. ; _item.name '<a href="#_diffrn_scan_frame.frame_number" >_diffrn_scan_frame.frame_number</a>' _item.category_id diffrn_scan_frame _item.mandatory_code no _item_type.code int loop_ _item_range.maximum _item_range.minimum . 0 0 0 save_ save_<a name="_diffrn_scan_frame.integration_time">_diffrn_scan_frame.integration_time</a> _item_description.description ; The time in seconds to integrate this step of the scan. This should be the precise time of integration of each particular frame. The value of this data item should be given explicitly for each frame and not inferred from the value of '<a href="#_diffrn_scan.integration_time" >_diffrn_scan.integration_time</a>'. ; _item.name '<a href="#_diffrn_scan_frame.integration_time" >_diffrn_scan_frame.integration_time</a>' _item.category_id diffrn_scan_frame _item.mandatory_code yes _item_type.code float _item_units.code 'seconds' loop_ _item_range.maximum _item_range.minimum . 0.0 save_ save_<a name="_diffrn_scan_frame.scan_id" >_diffrn_scan_frame.scan_id</a> _item_description.description ; The value of <a href="#_diffrn_scan_frame.scan_id" >_diffrn_scan_frame.scan_id</a> identifies the scan containing this frame. This item is a pointer to <a href="#_diffrn_scan.id" >_diffrn_scan.id</a> in the <a href="#DIFFRN_SCAN">DIFFRN_SCAN</a> category. ; _item.name '<A HREF="#_diffrn_scan_frame.scan_id">_diffrn_scan_frame.scan_id</A>' _item.category_id diffrn_scan_frame _item.mandatory_code yes save_ ########################## # <a name="DIFFRN_SCAN_FRAME_AXIS">DIFFRN_SCAN_FRAME_AXIS</a> # ########################## save_DIFFRN_SCAN_FRAME_AXIS _category.description ; Data items in the <a href="#DIFFRN_SCAN_FRAME_AXIS">DIFFRN_SCAN_FRAME_AXIS</a> category describe the settings of axes for particular frames. Unspecified axes are assumed to be at their zero points. If, for any given frame, non-zero values apply for any of the data items in this category, those values should be given explicitly in this category and not simply inferred from values in <a href="#DIFFRN_SCAN_AXIS">DIFFRN_SCAN_AXIS</a>. ; _category.id diffrn_scan_frame_axis _category.mandatory_code no loop_ _category_key.name '<a href="#_diffrn_scan_frame_axis.frame_id" >_diffrn_scan_frame_axis.frame_id</a>' '<a href="#_diffrn_scan_frame_axis.axis_id" >_diffrn_scan_frame_axis.axis_id</a>' loop_ _category_group.id 'inclusive_group' 'diffrn_group' save_ save_<a name="_diffrn_scan_frame_axis.axis_id" >_diffrn_scan_frame_axis.axis_id</a> _item_description.description ; The value of this data item is the identifier of one of the axes for the frame for which settings are being specified. Multiple axes may be specified for the same value of <a href="#_diffrn_scan_frame.id" >_diffrn_scan_frame.frame_id</a> This item is a pointer to <a href="#_axis.id" >_axis.id</a> in the <a href="#AXIS">AXIS</a> category. ; _item.name '<a href="#_diffrn_scan_frame_axis.axis_id" >_diffrn_scan_frame_axis.axis_id</a>' _item.category_id diffrn_scan_frame_axis _item.mandatory_code yes save_ save_<a name="_diffrn_scan_frame_axis.angle" >_diffrn_scan_frame_axis.angle</a> _item_description.description ; The setting of the specified axis in degrees for this frame. This is the setting at the start of the integration time. ; _item.name '<a href="#_diffrn_scan_frame_axis.angle" >_diffrn_scan_frame_axis.angle</a>' _item.category_id diffrn_scan_frame_axis _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'degrees' save_ save_<A NAME="_diffrn_scan_frame_axis.angle_increment">_diffrn_scan_frame_axis.angle_increment</A> _item_description.description ; The increment for this frame for angular setting of the specified axis in degrees. The sum of the values of '<A HREF="#_diffrn_scan_frame_axis.angle">_diffrn_scan_frame_axis.angle</A>' and '<A HREF="#_diffrn_scan_frame_axis.angle_increment">_diffrn_scan_frame_axis.angle_increment</A>' is the angular setting of the axis at the end of the integration time for this frame. ; _item.name '<A HREF="#_diffrn_scan_frame_axis.angle_increment">_diffrn_scan_frame_axis.angle_increment</A>' _item.category_id diffrn_scan_frame_axis _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'degrees' save_ save_<A NAME="_diffrn_scan_frame_axis.angle_rstrt_incr">_diffrn_scan_frame_axis.angle_rstrt_incr</A> _item_description.description ; The increment after this frame for angular setting of the specified axis in degrees. The sum of the values of '<A HREF="#_diffrn_scan_frame_axis.angle">_diffrn_scan_frame_axis.angle</A>' and '<A HREF="#_diffrn_scan_frame_axis.angle_increment">_diffrn_scan_frame_axis.angle_increment</A>' and '<A HREF="#_diffrn_scan_frame_axis.angle_rstrt_incr">_diffrn_scan_frame_axis.angle_rstrt_incr</A>' is the angular setting of the axis at the start of the integration time for the next frame, and should equal '<A HREF="#_diffrn_scan_frame_axis.angle">_diffrn_scan_frame_axis.angle</A>' for that next frame. ; _item.name '<A HREF="#_diffrn_scan_frame_axis.angle_rstrt_incr">_diffrn_scan_frame_axis.angle_rstrt_incr</A>' _item.category_id diffrn_scan_frame_axis _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'degrees' save_ save_<a name="_diffrn_scan_frame_axis.displacement" >_diffrn_scan_frame_axis.displacement</a> _item_description.description ; The setting of the specified axis in millimetres for this frame. This is the setting at the start of the integration time. ; _item.name '<a href="#_diffrn_scan_frame_axis.displacement" >_diffrn_scan_frame_axis.displacement</a>' _item.category_id diffrn_scan_frame_axis _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'millimetres' save_ save_<A NAME="_diffrn_scan_frame_axis.displacement_increment">_diffrn_scan_frame_axis.displacement_increment</A> _item_description.description ; The increment for this frame for displacement setting of the specified axis in millimetres. The sum of the values of '<A HREF="#_diffrn_scan_frame_axis.displacement">_diffrn_scan_frame_axis.displacement</A>' and '<A HREF="#_diffrn_scan_frame_axis.displacement_increment">_diffrn_scan_frame_axis.displacement_increment</A>' is the angular setting of the axis at the end of the integration time for this frame. ; _item.name '<A HREF="#_diffrn_scan_frame_axis.displacement_increment">_diffrn_scan_frame_axis.displacement_increment</A>' _item.category_id diffrn_scan_frame_axis _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'millimetres' save_ save_<A NAME="_diffrn_scan_frame_axis.displacement_rstrt_incr">_diffrn_scan_frame_axis.displacement_rstrt_incr</A> _item_description.description ; The increment for this frame for displacement setting of the specified axis in millimetres. The sum of the values of '<A HREF="#_diffrn_scan_frame_axis.displacement">_diffrn_scan_frame_axis.displacement</A>' and '<A HREF="#_diffrn_scan_frame_axis.displacement_increment">_diffrn_scan_frame_axis.displacement_increment</A>' and '<A HREF="#_diffrn_scan_frame_axis.displacement_rstrt_incr">_diffrn_scan_frame_axis.displacement_rstrt_incr</A>' is the angular setting of the axis at the start of the integration time for the next frame, and should equal '<A HREF="#_diffrn_scan_frame_axis.displacement">_diffrn_scan_frame_axis.displacement</A>' for that next frame. ; _item.name '<A HREF="#_diffrn_scan_frame_axis.displacement_rstrt_incr">_diffrn_scan_frame_axis.displacement_rstrt_incr</A>' _item.category_id diffrn_scan_frame_axis _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'millimetres' save_ save_<a name="_diffrn_scan_frame_axis.frame_id" >_diffrn_scan_frame_axis.frame_id</a> _item_description.description ; The value of this data item is the identifier of the frame for which axis settings are being specified. Multiple axes may be specified for the same value of <a href="#_diffrn_scan_frame.frame_id" >_diffrn_scan_frame.frame_id</a> . This item is a pointer to <a href="#_diffrn_data_frame.id" >_diffrn_data_frame.id</a> in the <a href="#DIFFRN_DATA_FRAME">DIFFRN_DATA_FRAME</a> category. ; _item.name '<a href="#_diffrn_scan_frame_axis.frame_id" >_diffrn_scan_frame_axis.frame_id</a>' _item.category_id diffrn_scan_frame_axis _item.mandatory_code yes save_ #################### ## <A NAME="ITEM_TYPE_LIST">ITEM_TYPE_LIST</A> ## #################### # # # The regular expressions defined here are not compliant # with the POSIX 1003.2 standard as they include the # '\n' and '\t' special characters. These regular expressions # have been tested using version 0.12 of Richard Stallman's # GNU regular expression library in POSIX mode. # In order to allow presentation of a regular expression # in a text field concatenate any line ending in a backslash # with the following line, after discarding the backslash. # # A formal definition of the '\n' and '\t' special characters # is most properly done in the DDL, but for completeness, please # note that '\n' is the line termination character ('newline') # and '\t' is the horizontal tab character. There is a formal # ambiguity in the use of '\n' for line termination, in that # the intention is that the equivalent machine/OS-dependent line # termination character sequence should be accepted as a match, e.g. # # '\r' (control-M) under MacOS # '\n' (control-J) under Unix # '\r\n' (control-M control-J) under DOS and MS Windows # loop_ _item_type_list.code _item_type_list.primitive_code _item_type_list.construct _item_type_list.detail code char '[_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*' ; code item types/single words ... ; ucode uchar '[_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*' ; code item types/single words (case insensitive) ; line char '[][ \t_(),.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*' ; code item types / multi-word items ... ; uline uchar '[][ \t_(),.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*' ; code item types / multi-word items (case insensitive) ; text char '[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*' ; text item types / multi-line text ... ; binary char ;\n--CIF-BINARY-FORMAT-SECTION--\n\ [][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*\ \n--CIF-BINARY-FORMAT-SECTION---- ; ; binary items are presented as MIME-like ascii-encoded sections in an imgCIF. In a CBF, raw octet streams are used to convey the same information. ; int numb '-?[0-9]+' ; int item types are the subset of numbers that are the negative or positive integers. ; float numb '-?(([0-9]+)|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)?' ; float item types are the subset of numbers that are the floating numbers. ; any char '.*' ; A catch all for items that may take any form... ; yyyy-mm-dd char ;\ [0-9]?[0-9]?[0-9][0-9]-[0-9]?[0-9]-[0-9][0-9]\ (T[0-2][0-9]:[0-5][0-9]:[0-5][0-9](.[0-9]+)([+-][0-5][0-9]:[0-5][0-9])) ; ; Standard format for CIF date and time strings (see http://www.iucr.orgiucr-top/cif/spec/datetime.html), consisting of a yyyy-mm-dd date optionally followed by the character "T" followed by a 24-hour clock time, optionally followed by a signed time-zone offset. The IUCr standard has been extended to allow for an optional decimal fraction on the seconds of time. Time is local time if no time-zone offset is given. ; ##################### ## <a name="ITEM_UNITS_LIST">ITEM_UNITS_LIST</a> ## ##################### loop_ _item_units_list.code _item_units_list.detail # 'metres' 'metres' 'centimetres' 'centimetres (metres * 10^( -2))' 'millimetres' 'millimetres (metres * 10^( -3))' 'nanometres' 'nanometres (metres * 10^( -9))' 'angstroms' 'angstroms (metres * 10^(-10))' 'picometres' 'picometres (metres * 10^(-12))' 'femtometres' 'femtometres (metres * 10^(-15))' # 'reciprocal_metres' 'reciprocal metres (metres^(-1))' 'reciprocal_centimetres' 'reciprocal centimetres ((metres * 10^( -2))^(-1))' 'reciprocal_millimetres' 'reciprocal millimetres ((metres * 10^( -3))^(-1))' 'reciprocal_nanometres' 'reciprocal nanometres ((metres * 10^( -9))^(-1))' 'reciprocal_angstroms' 'reciprocal angstroms ((metres * 10^(-10))^(-1))' 'reciprocal_picometres' 'reciprocal picometres ((metres * 10^(-12))^(-1))' 'reciprocal_metres' 'reciprocal metres (metres * 10^-1)' 'reciprocal_centimetres' 'reciprocal centimetres (metres * 10^( -2)^-1)' 'reciprocal_millimetres' 'reciprocal millimetres (metres * 10^( -3)^-1)' 'reciprocal_nanometres' 'reciprocal nanometres (metres * 10^( -9)^-1)' 'reciprocal_angstroms' 'reciprocal angstroms (metres * 10^(-10)^-1)' 'reciprocal_picometres' 'reciprocal picometres (metres * 10^(-12)^-1)' # 'nanometres_squared' 'nanometres squared (metres * 10^( -9))^2' 'angstroms_squared' 'angstroms squared (metres * 10^(-10))^2' '8pi2_angstroms_squared' '8pi^2 * angstroms squared (metres * 10^(-10))^2' 'picometres_squared' 'picometres squared (metres * 10^(-12))^2' # 'nanometres_cubed' 'nanometres cubed (metres * 10^( -9))^3' 'angstroms_cubed' 'angstroms cubed (metres * 10^(-10))^3' 'picometres_cubed' 'picometres cubed (metres * 10^(-12))^3' # 'kilopascals' 'kilopascals' 'gigapascals' 'gigapascals' # 'hours' 'hours' 'minutes' 'minutes' 'seconds' 'seconds' 'microseconds' 'microseconds' # 'degrees' 'degrees (of arc)' 'degrees_squared' 'degrees (of arc) squared' # 'degrees_per_minute' 'degrees (of arc) per minute' # 'celsius' 'degrees (of temperature) Celsius' 'kelvins' 'degrees (of temperature) Kelvin' # 'counts' 'counts' 'counts_per_photon' 'counts per photon' # 'electrons' 'electrons' # 'electrons_squared' 'electrons squared' # 'electrons_per_nanometres_cubed' ; electrons per nanometres cubed (electrons/(metres * 10^( -9))^(-3)) ; 'electrons_per_angstroms_cubed' ; electrons per nanometres cubed (electrons/(metres * 10^(-10))^(-3)); ; 'electrons_per_picometres_cubed' ; electrons per nanometres cubed (electrons/(metres * 10^(-12))^(-3)); ; 'kilowatts' 'kilowatts' 'milliamperes' 'milliamperes' 'kilovolts' 'kilovolts' # 'arbitrary' ; arbitrary system of units. ; # loop_ _item_units_conversion.from_code _item_units_conversion.to_code _item_units_conversion.operator _item_units_conversion.factor ### 'metres' 'centimetres' '*' 1.0E+02 'metres' 'millimetres' '*' 1.0E+03 'metres' 'nanometres' '*' 1.0E+09 'metres' 'angstroms' '*' 1.0E+10 'metres' 'picometres' '*' 1.0E+12 'metres' 'femtometres' '*' 1.0E+15 # 'centimetres' 'metres' '*' 1.0E-02 'centimetres' 'millimetres' '*' 1.0E+01 'centimetres' 'nanometres' '*' 1.0E+07 'centimetres' 'angstroms' '*' 1.0E+08 'centimetres' 'picometres' '*' 1.0E+10 'centimetres' 'femtometres' '*' 1.0E+13 # 'millimetres' 'metres' '*' 1.0E-03 'millimetres' 'centimetres' '*' 1.0E-01 'millimetres' 'nanometres' '*' 1.0E+06 'millimetres' 'angstroms' '*' 1.0E+07 'millimetres' 'picometres' '*' 1.0E+09 'millimetres' 'femtometres' '*' 1.0E+12 # 'nanometres' 'metres' '*' 1.0E-09 'nanometres' 'centimetres' '*' 1.0E-07 'nanometres' 'millimetres' '*' 1.0E-06 'nanometres' 'angstroms' '*' 1.0E+01 'nanometres' 'picometres' '*' 1.0E+03 'nanometres' 'femtometres' '*' 1.0E+06 # 'angstroms' 'metres' '*' 1.0E-10 'angstroms' 'centimetres' '*' 1.0E-08 'angstroms' 'millimetres' '*' 1.0E-07 'angstroms' 'nanometres' '*' 1.0E-01 'angstroms' 'picometres' '*' 1.0E+02 'angstroms' 'femtometres' '*' 1.0E+05 # 'picometres' 'metres' '*' 1.0E-12 'picometres' 'centimetres' '*' 1.0E-10 'picometres' 'millimetres' '*' 1.0E-09 'picometres' 'nanometres' '*' 1.0E-03 'picometres' 'angstroms' '*' 1.0E-02 'picometres' 'femtometres' '*' 1.0E+03 # 'femtometres' 'metres' '*' 1.0E-15 'femtometres' 'centimetres' '*' 1.0E-13 'femtometres' 'millimetres' '*' 1.0E-12 'femtometres' 'nanometres' '*' 1.0E-06 'femtometres' 'angstroms' '*' 1.0E-05 'femtometres' 'picometres' '*' 1.0E-03 ### 'reciprocal_centimetres' 'reciprocal_metres' '*' 1.0E+02 'reciprocal_centimetres' 'reciprocal_millimetres' '*' 1.0E-01 'reciprocal_centimetres' 'reciprocal_nanometres' '*' 1.0E-07 'reciprocal_centimetres' 'reciprocal_angstroms' '*' 1.0E-08 'reciprocal_centimetres' 'reciprocal_picometres' '*' 1.0E-10 # 'reciprocal_millimetres' 'reciprocal_metres' '*' 1.0E+03 'reciprocal_millimetres' 'reciprocal_centimetres' '*' 1.0E+01 'reciprocal_millimetres' 'reciprocal_nanometres' '*' 1.0E-06 'reciprocal_millimetres' 'reciprocal_angstroms' '*' 1.0E-07 'reciprocal_millimetres' 'reciprocal_picometres' '*' 1.0E-09 # 'reciprocal_nanometres' 'reciprocal_metres' '*' 1.0E+09 'reciprocal_nanometres' 'reciprocal_centimetres' '*' 1.0E+07 'reciprocal_nanometres' 'reciprocal_millimetres' '*' 1.0E+06 'reciprocal_nanometres' 'reciprocal_angstroms' '*' 1.0E-01 'reciprocal_nanometres' 'reciprocal_picometres' '*' 1.0E-03 # 'reciprocal_angstroms' 'reciprocal_metres' '*' 1.0E+10 'reciprocal_angstroms' 'reciprocal_centimetres' '*' 1.0E+08 'reciprocal_angstroms' 'reciprocal_millimetres' '*' 1.0E+07 'reciprocal_angstroms' 'reciprocal_nanometres' '*' 1.0E+01 'reciprocal_angstroms' 'reciprocal_picometres' '*' 1.0E-02 # 'reciprocal_picometres' 'reciprocal_metres' '*' 1.0E+12 'reciprocal_picometres' 'reciprocal_centimetres' '*' 1.0E+10 'reciprocal_picometres' 'reciprocal_millimetres' '*' 1.0E+09 'reciprocal_picometres' 'reciprocal_nanometres' '*' 1.0E+03 'reciprocal_picometres' 'reciprocal_angstroms' '*' 1.0E+01 ### 'nanometres_squared' 'angstroms_squared' '*' 1.0E+02 'nanometres_squared' 'picometres_squared' '*' 1.0E+06 # 'angstroms_squared' 'nanometres_squared' '*' 1.0E-02 'angstroms_squared' 'picometres_squared' '*' 1.0E+04 'angstroms_squared' '8pi2_angstroms_squared' '*' 78.9568 # 'picometres_squared' 'nanometres_squared' '*' 1.0E-06 'picometres_squared' 'angstroms_squared' '*' 1.0E-04 ### 'nanometres_cubed' 'angstroms_cubed' '*' 1.0E+03 'nanometres_cubed' 'picometres_cubed' '*' 1.0E+09 # 'angstroms_cubed' 'nanometres_cubed' '*' 1.0E-03 'angstroms_cubed' 'picometres_cubed' '*' 1.0E+06 # 'picometres_cubed' 'nanometres_cubed' '*' 1.0E-09 'picometres_cubed' 'angstroms_cubed' '*' 1.0E-06 ### 'kilopascals' 'gigapascals' '*' 1.0E-06 'gigapascals' 'kilopascals' '*' 1.0E+06 ### 'hours' 'minutes' '*' 6.0E+01 'hours' 'seconds' '*' 3.6E+03 'hours' 'microseconds' '*' 3.6E+09 # 'minutes' 'hours' '/' 6.0E+01 'minutes' 'seconds' '*' 6.0E+01 'minutes' 'microseconds' '*' 6.0E+07 # 'seconds' 'hours' '/' 3.6E+03 'seconds' 'minutes' '/' 6.0E+01 'seconds' 'microseconds' '*' 1.0E+06 # 'microseconds' 'hours' '/' 3.6E+09 'microseconds' 'minutes' '/' 6.0E+07 'microseconds' 'seconds' '/' 1.0E+06 ### 'celsius' 'kelvins' '-' 273.0 'kelvins' 'celsius' '+' 273.0 ### 'electrons_per_nanometres_cubed' 'electrons_per_angstroms_cubed' '*' 1.0E+03 'electrons_per_nanometres_cubed' 'electrons_per_picometres_cubed' '*' 1.0E+09 # 'electrons_per_angstroms_cubed' 'electrons_per_nanometres_cubed' '*' 1.0E-03 'electrons_per_angstroms_cubed' 'electrons_per_picometres_cubed' '*' 1.0E+06 # 'electrons_per_picometres_cubed' 'electrons_per_nanometres_cubed' '*' 1.0E-09 'electrons_per_picometres_cubed' 'electrons_per_angstroms_cubed' '*' 1.0E-06 ### ######################## ## <a name="DICTIONARY_HISTORY">DICTIONARY_HISTORY</a> ## ######################## loop_ _dictionary_history.version _dictionary_history.update _dictionary_history.revision 1.2.3 2003-07-03 ; Cleanup to conform to ITVG. + Correct sign error in ..._cubed units. + Correct '_diffrn_radiation.polarisn_norm' range. (HJB) ; 1.2.2 2003-03-10 ; Correction of typos in various DIFFRN_SCAN_AXIS descriptions. (HJB) ; 1.2.1 2003-02-22 ; Correction of ATOM_ for ARRAY_ typos in various descriptions. (HJB) ; 1.2 2003-02-07 ; Corrections to encodings (remove extraneous hyphens) remove extraneous underscore in _array_structure.encoding_type enumeration. Correct typos in items units list. (HJB) ; 1.1.3 2001-04-19 ; Another typo corrections by Wilfred Li, and cleanup by HJB ; 1.1.2 2001-03-06 ; Several typo corrections by Wilfred Li ; 1.1.1 2001-02-16 ; Several typo corrections by JW ; 1.1 2001-02-06 ; Draft resulting from discussions on header for use at NSLS (HJB) + Change DIFFRN_FRAME_DATA to <A HREF="#DIFFRN_DATA_FRAME">DIFFRN_DATA_FRAME</A> + Change '_diffrn_detector_axis.id' to '<A HREF="#_diffrn_detector_axis.detector_id">_diffrn_detector_axis.detector_id</A>'. + Add '<A HREF="#_diffrn_measurement_axis.measurement_device">_diffrn_measurement_axis.measurement_device</A>' and change '_diffrn_measurement_axis.id' to '<A HREF="#_diffrn_measurement_axis.measurement_id">_diffrn_measurement_axis.measurement_id</A>'. + Add '<A HREF="#_diffrn_radiation.div_x_source">_diffrn_radiation.div_x_source</A>', '<A HREF="#_diffrn_radiation.div_y_source">_diffrn_radiation.div_y_source</A>', '<A HREF="#_diffrn_radiation.div_x_y_source">_diffrn_radiation.div_x_y_source</A>', '<A HREF="#_diffrn_radiation.polarizn_source_norm">_diffrn_radiation.polarizn_source_norm</A>', '<A HREF="#_diffrn_radiation.polarizn_source_ratio">_diffrn_radiation.polarizn_source_ratio</A>', '<A HREF="#_diffrn_scan.date_end">_diffrn_scan.date_end</A>', '<A HREF="#_diffrn_scan.date_start">_diffrn_scan.date_start</A>', '<A HREF="#_diffrn_scan_axis.angle_rstrt_incr">_diffrn_scan_axis.angle_rstrt_incr</A>', '<A HREF="#_diffrn_scan_axis.displacement_rstrt_incr">_diffrn_scan_axis.displacement_rstrt_incr</A>', '<A HREF="#_diffrn_scan_frame_axis.angle_increment">_diffrn_scan_frame_axis.angle_increment</A>', '<A HREF="#_diffrn_scan_frame_axis.angle_rstrt_incr">_diffrn_scan_frame_axis.angle_rstrt_incr</A>', '<A HREF="#_diffrn_scan_frame_axis.displacement">_diffrn_scan_frame_axis.displacement</A>', '<A HREF="#_diffrn_scan_frame_axis.displacement_increment">_diffrn_scan_frame_axis.displacement_increment</A>',and '<A HREF="#_diffrn_scan_frame_axis.displacement_rstrt_incr">_diffrn_scan_frame_axis.displacement_rstrt_incr</A>'. + Add <A HREF="#_diffrn_measurement.device">_diffrn_measurement.device</A> to category key + Update yyyy-mm-dd to allow optional time with fractional seconds for time stamps. + Fix typos caught by RS. + Add <a href="#ARRAY_STRUCTURE_LIST_AXIS">ARRAY_STRUCTURE_LIST_AXIS</a> category, and use concept of axis sets to allow for coupled axes, as in spiral scans. + Add examples for fairly complete headers thanks to R. Sweet and P. Ellis. ; 1.0 2000-12-21 ; Release version - few typos and tidying up (BM & HJB) + Move ITEM_TYPE_LIST, ITEM_UNITS_LIST and DICTIONARY_HISTORY to end of dictionary. + Alphabetize dictionary. ; 0.7.1 2000-09-29 ; Cleanup fixes (JW) + Correct spelling of diffrn_measurement_axis in <a href="#_axis.id">_axis.id</a> + Correct ordering of uses of _item.mandatory_code and _item_default.value ; 0.7.0 2000-09-09 ; Respond to comments by I. David Brown (HJB) + Added further comments on '\n' and '\t' + Updated ITEM_UNITS_LIST by taking section from mmCIF dictionary and adding metres. Changed all spelling 'meter' to 'metre' throughout. + Added missing enumerations to <a href="#_array_structure.compression_type">_array_structure.compression_type</a> and made 'none' the default. + Removed parent-child relationship between <a href="#_array_structure_list.index">_array_structure_list.index</a> and <a href="#_array_structure_list.precedence">_array_structure_list.precedence</a> . + Improve alphabetization. + Fix <a href="#_array_intensities.gain_esd">_array_intensities_gain.esd</a> related function. + Improved comments in <a href="#AXIS">AXIS</a>. + Fixed DIFFRN_FRAME_DATA example. + Removed erroneous <a href="#DIFFRN_MEASUREMENT">DIFFRN_MEASUREMENT</a> example. + Added <a href="#_diffrn_measurement_axis.id">_diffrn_measurement_axis.id</a> to the category key. ; 0.6.0 1999-01-14 ; Remove redundant information for ENC_NONE data (HJB) + After the D5 remove binary section identifier, size and compression type. + Add Control-L to header. ; 0.5.1 1999-01-03 ; Cleanup of typos and syntax errors (HJB) + Cleanup example details for <a href="#DIFFRN_SCAN">DIFFRN_SCAN</a> category. + Add missing quote marks for <a href="#_diffrn_scan.id" >_diffrn_scan.id</a> definition. ; 0.5 1999-01-01 ; Modifications for axis definitions and reduction of binary header (HJB) + Restored <a href="#_diffrn_detector.diffrn_id" >_diffrn_detector.diffrn_id</a> to <A HREF="#DIFFRN_DETECTOR">DIFFRN_DETECTOR</A> KEY. + Added <a href="#AXIS">AXIS</a> category. + Brought complete <A HREF="#DIFFRN_DETECTOR">DIFFRN_DETECTOR</A> and <a href="#DIFFRN_MEASUREMENT">DIFFRN_MEASUREMENT</a> categories in from cif_mm.dic for clarity. + changed _array_structure.encoding_type from type code to uline and added X-Binary-Element-Type to MIME header. + added detector beam center <a href="#_diffrn_detector_element.center[1]" >_diffrn_detector_element.center[1]</a> and <a href="#_diffrn_detector_element.center[2]" >_diffrn_detector_element.center[2]</a> + corrected item name of <a href="#_diffrn_refln.frame_id" >_diffrn_refln.frame_id</a> + replace reference to _array_intensities.undefined by _array_intensities.undefined_value + replace references to _array_intensity.scaling with _array_intensities.scaling + added <a href="#DIFFRN_SCAN">DIFFRN_SCAN</a>... categories ; 0.4 1998-08-11 ; Modifications to the 0.3 imgCIF draft (HJB) + Reflowed comment lines over 80 characters and corrected typos. + Updated examples and descriptions of MIME encoded data. + Change name to cbfext98.dic. ; 0.3 1998-07-04 ; Modifications for imgCIF (HJB) + Added binary type, which is a text field containing a variant on MIME encoded data. + Changed type of <a href="#_array_data.data" >_array_data.data</a> to binary and specified internal structure of raw binary data. + Added <a href="#_array_data.binary_id" >_array_data.binary_id</a>, and made <a href="#_diffrn_frame_data.binary_id" >_diffrn_frame_data.binary_id</a> and <a href="#_array_intensities.binary_id" >_array_intensities.binary_id</a> into pointers to this item. ; 0.2 1997-12-02 ; Modifications to the CBF draft (JW): + Added category hierarchy for describing frame data developed from discussions at the BNL imgCIF Workshop Oct 1997. The following changes were made in implementing the workshop draft. Category DIFFRN_ARRAY_DATA was renamed to DIFFRN_FRAME_DATA. Category DIFFRN_FRAME_TYPE was renamed to <a href="#DIFFRN_DETECTOR_ELEMENT">DIFFRN_DETECTOR_ELEMENT</a>. The parent item for <a href="#_diffrn_frame_data.array_id" >_diffrn_frame_data.array_id</a> was changed from array_structure_list.array_id to array_structure.id. Item _diffrn_detector.array_id was deleted. + Added data item <a href="#_diffrn_frame_data.binary_id" >_diffrn_frame_data.binary_id</a> to identify data groups within a binary section. The formal identification of the binary section is still fuzzy. ; 0.1 1997-01-24 ; First draft of this dictionary in DDL 2.1 compliant format by John Westbrook (JW). This version was adapted from the Crystallographic Binary File (CBF) Format Draft Proposal provided by Andy Hammersley (AH). Modifications to the CBF draft (JW): + In this version the array description has been cast in the categories <A HREF="#ARRAY_STRUCTURE">ARRAY_STRUCTURE</A> and <A HREF="#ARRAY_STRUCTURE_LIST">ARRAY_STRUCTURE_LIST</A>. These categories have been generalized to describe array data of arbitrary dimension. + Array data in this description are contained in the category <a href="#ARRAY_DATA">ARRAY_DATA</a> . This departs from the CBF notion of data existing in some special comment. In this description, data is handled as an ordinary data item encapsulated in a character data type. Although handling binary data this manner deviates from CIF conventions, it does not violate any DDL 2.1 rules. DDL 2.1 regular expressions can be used to define the binary representation which will permit some level of data validation. In this version, the placeholder type code "any" has been used. This translates to a regular expression which will match any pattern. It should be noted that DDL 2.1 already supports array data objects although these have not been used in the current mmCIF dictionary. It may be possible to use the DDL 2.1 ITEM_STRUCTURE and ITEM_STRUCTURE_LIST categories to provide the information that is carried in by the <a href="#ARRAY_STRUCTURE">ARRAY_STRUCTURE</a> and <a href="#ARRAY_STRUCTURE_LIST">ARRAY_STRUCTURE_LIST</a>. By moving the array structure to the DDL level it would be possible to define an array type as well as a regular expression defining the data format. + Multiple array sections can be properly handled within a single datablock. ; #-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof </PRE> </BODY> </HTML>