Data Item


Item name
Category name
Attribute name
Required in PDB entries
Used in currrent PDB entries

Item Description

The value of contains the array data encapsulated in a STAR string. The representation used is a variant on the Multipurpose Internet Mail Extensions (MIME) specified in RFC 2045-2049 by N. Freed et al. The boundary delimiter used in writing an imgCIF or CBF is '\n--CIF-BINARY-FORMAT-SECTION--' (including the required initial '\n--'). The Content-Type may be any of the discrete types permitted in RFC 2045; 'application/octet-stream' is recommended for diffraction images in the ARRAY_DATA category. Note: When appropriate in other categories, e.g. for photographs of crystals, more precise types, such as 'image/jpeg', 'image/tiff', 'image/png', etc. should be used. 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"' or the parameter 'conversions="X-CBF_BYTE_OFFSET"' or the parameter 'conversions="X-CBF_BACKGROUND_OFFSET_DELTA"' If the parameter 'conversions="X-CBF_PACKED"' is given it may be further modified with the parameters '"uncorrelated_sections"' or '"flat"' If the '"uncorrelated_sections"' parameter is given, each section will be compressed without using the prior section for averaging. If the '"flat"' parameter is given, each the image will be treated as one long row. Note that the X-CBF_CANONICAL and X-CBF_PACKED are slower but more efficient compressions that the others. The X-CBF_BYTE_OFFSET compression is a good compromise between speed and efficiency for ordinary diffraction images. The X-CBF_BACKGROUND_OFFSET_DELTA compression is oriented towards sparse data, such as masks and tables of replacement pixel values for images with overloaded spots. The Content-Transfer-Encoding may be 'BASE64', 'Quoted-Printable', 'X-BASE8', 'X-BASE10', 'X-BASE16' or 'X-BASE32K', for an imgCIF or 'BINARY' for a CBF. The octal, decimal and hexadecimal transfer encodings are provided for convenience in debugging and are not recommended for archiving and data interchange. In a CIF, one of the parameters 'charset=us-ascii', 'charset=utf-8' or 'charset=utf-16' may be used on the Content-Transfer-Encoding to specify the character set used for the external presentation of the encoded data. If no charset parameter is given, the character set of the enclosing CIF is assumed. In any case, if a BOM flag is detected (FE FF for big-endian UTF-16, FF FE for little-endian UTF-16 or EF BB BF for UTF-8) is detected, the indicated charset will be assumed until the end of the encoded data or the detection of a different BOM. The charset of the Content-Transfer-Encoding is not the character set of the encoded data, only the character set of the presentation of the encoded data and should be respecified for each distinct STAR string. In an imgCIF file, the encoded binary data begins after the empty line terminating the header. In an imgCIF file, the encoded binary data ends with the terminating boundary delimiter '\n--CIF-BINARY-FORMAT-SECTION----' in the currently effective charset or with the '\n; ' that terminates the STAR string. In a CBF, the raw binary data begins after an empty line terminating the header and after the sequence: Octet Hex Decimal Purpose 0 0C 12 (ctrl-L) Page break 1 1A 26 (ctrl-Z) Stop listings in MS-DOS 2 04 04 (Ctrl-D) Stop listings in UNIX 3 D5 213 Binary section begins None of these octets are included in the calculation of the message size or in the calculation of the message digest. The X-Binary-Size header specifies the size of the equivalent binary data in octets. If compression was used, this size is the size after compression, including any book-keeping fields. An adjustment is made for the deprecated binary formats in which eight bytes of binary header are used for the compression type. In this case, the eight bytes used for the compression type are subtracted from the size, so that the same size will be reported if the compression type is supplied in the MIME header. Use of the MIME header is the recommended way to supply the compression type. In general, no portion of the binary header is included in the calculation of the size. The X-Binary-Element-Type header specifies the type of binary data in the octets, using the same descriptive phrases as in _array_structure.encoding_type. The default value is 'unsigned 32-bit integer'. An MD5 message digest may, optionally, be used. The 'RSA Data Security, Inc. MD5 Message-Digest Algorithm' should be used. No portion of the header is included in the calculation of the message digest. If the Transfer Encoding is 'X-BASE8', 'X-BASE10' or 'X-BASE16', the data are presented as octal, decimal or hexadecimal data organized into lines or words. Each word is created by composing octets of data in fixed groups of 2, 3, 4, 6 or 8 octets, either in the order ...4321 ('big- endian') or 1234... ('little-endian'). If there are fewer than the specified number of octets to fill the last word, then the missing octets are presented as '==' for each missing octet. Exactly two equal signs are used for each missing octet even for octal and decimal encoding. The format of lines is: rnd xxxxxx xxxxxx xxxxxx where r is 'H', 'O' or 'D' for hexadecimal, octal or decimal, n is the number of octets per word and d is '<' or '>' for the '...4321' and '1234...' octet orderings, respectively. The '==' padding for the last word should be on the appropriate side to correspond to the missing octets, e.g. H4< FFFFFFFF FFFFFFFF 07FFFFFF ====0000 or H3> FF0700 00==== For these hexadecimal, octal and decimal formats only, comments beginning with '#' are permitted to improve readability. BASE64 encoding follows MIME conventions. Octets are in groups of three: c1, c2, c3. The resulting 24 bits are broken into four six-bit quantities, starting with the high-order six bits (c1 >> 2) of the first octet, then the low-order two bits of the first octet followed by the high-order four bits of the second octet [(c1 & 3)<<4 | (c2>>4)], then the bottom four bits of the second octet followed by the high-order two bits of the last octet [(c2 & 15)<<2 | (c3>>6)], then the bottom six bits of the last octet (c3 & 63). Each of these four quantities is translated into an ASCII character using the mapping: 1 2 3 4 5 6 0123456789012345678901234567890123456789012345678901234567890123 | | | | | | | ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/ With short groups of octets padded on the right with one '=' if c3 is missing, and with '==' if both c2 and c3 are missing. X-BASE32K encoding is similar to BASE64 encoding, except that sets of 15 octets are encoded as sets of 8 16-bit unicode characters, by breaking the 120 bits into 8 15-bit quantities. 256 is added to each 15 bit quantity to bring it into a printable uncode range. When encoding, zero padding is used to fill out the last 15 bit quantity. If 8 or more bits of padding are used, a single equals sign (hexadecimal 003D) is appended. Embedded whitespace and newlines are introduced to produce lines of no more than 80 characters each. On decoding, all printable ascii characters and ascii whitespace characters are ignored except for any trailing equals signs. The number of trailing equals signs indicated the number of trailing octets to be trimmed from the end of the decoded data. (see Georgi Darakev, Vassil Litchev, Kostadin Z. Mitev, Herbert J. Bernstein, 'Efficient Support of Binary Data in the XML Implementation of the NeXus File Format',absract W0165, ACA Summer Meeting, Honolulu, HI, July 2006). QUOTED-PRINTABLE encoding also follows MIME conventions, copying octets without translation if their ASCII values are 32...38, 42, 48...57, 59, 60, 62, 64...126 and the octet is not a ';' in column 1. All other characters are translated to =nn, where nn is the hexadecimal encoding of the octet. All lines are 'wrapped' with a terminating '=' (i.e. the MIME conventions for an implicit line terminator are never used). The "X-Binary-Element-Byte-Order" can specify either '"BIG_ENDIAN"' or '"LITTLE_ENDIAN"' byte order of the imaage data. Only LITTLE_ENDIAN is recommended. Processors may treat BIG_ENDIAN as a warning of data that can only be processed by special software. The "X-Binary-Number-of-Elements" specifies the number of elements (not the number of octets) in the decompressed, decoded image. The optional "X-Binary-Size-Fastest-Dimension" specifies the number of elements (not the number of octets) in one row of the fastest changing dimension of the binary data array. This information must be in the MIME header for proper operation of some of the decompression algorithms. The optional "X-Binary-Size-Second-Dimension" specifies the number of elements (not the number of octets) in one column of the second-fastest changing dimension of the binary data array. This information must be in the MIME header for proper operation of some of the decompression algorithms. The optional "X-Binary-Size-Third-Dimension" specifies the number of sections for the third-fastest changing dimension of the binary data array. The optional "X-Binary-Size-Padding" specifies the size in octets of an optional padding after the binary array data and before the closing flags for a binary section.

Data Type

Data type code
Data type detail
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.
Primitive data type code
Regular expression
\n--CIF-BINARY-FORMAT-SECTION--\n\ [][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*\ \n--CIF-BINARY-FORMAT-SECTION----