#------------------------------------------------------------------------------ #$Date: 2012-04-12 15:13:32 +0000 (Thu, 12 Apr 2012) $ #$Revision: 52625 $ #$URL: file:///home/coder/svn-repositories/cod/cif/dictionaries/cif_cod.dic $ #------------------------------------------------------------------------------ # # This file is available in the Crystallography Open Database (COD), # http://www.crystallography.net/. # # This file is designated by the COD Advisory board into Public Domain. #------------------------------------------------------------------------------ data_on_this_dictionary _dictionary_name cif_cod.dic _dictionary_version 0.013 _dictionary_update 2011-09-22 _dictionary_history ; 2012-04-12 Adding the _cod_enantiomer_of data item definition. S.G 2011-09-22 Adjusting the _cod_original_sg_symbol_... tag names. S.G. 2011-09-20 Adding the _cod_database_fobs_code and _cod_database_coordinates_code tags. 2011-04-28 Improving formatting and correcting the definition syntax of the _cod_error_source data name. 2011-04-28 Adding descriptions for most of the rest of COD tags, new and old. 2011-04-28 Changing _dictionary_version value from 0.0.6 to 0.008 (removing the second decimal point and incrementing revision); the number is now decimal fraction to match definition in ddl1_core.dic. For versioning, we will from now on use the Perl versioning convention: versions will be floating point numbers with three digits allocated (0.007, 1.000, 1.021). Sub-minor revision can be indicated as extra two decimal places (e.g. 0.00701, 1.02102). Revisions can be compared numerically, as decimal fractions (so 0.007 < 0.00701, 0.00701 < 1.021, 1.021 < 1.02102 and so on). 2011-04-08 Adding descriptions of _cod_related_[] category. Commenting all tags with their despciprions from that category. Adding descriptions of the following tags: _cod_cif_authors_sg_H-M, _cod_cif_authors_sg_Hall _cod_cif_authors_sg_number, _cod_data_source_MD5_sum _cod_data_source_SHA1_sum, _cod_data_source_SHA256_sum 2011-04-06 Adding data names to the _cod_original_[] category. Adding _cod_chemical_formula_moiety_orig tag that is old-fashioned, its alternate name is _cod_original_formula_moiety tag. Adding _cod_chemical_formula_sum_orig tag that is old-fashioned, its alternate name is _cod_original_formula_sum. 2010-12-29 Adding descriptions of _cod_error_source and _cod_error_description tags. S.G. 2010-12-29 Adding description of the _cod_original_cell_volume tag and of the _cod_original_[] category. S.G. 2010-12-28 Adding description of the _cod_depositor_comments tag. S.G. 2009-06-13 Putting all private COD tags used at the moment. S.G. ; data_cod_enantiomer_of _name '_cod_enantiomer_of' _type char _definition ; Tells that the data block containing this value describes a structure that is an enantiomer of he structure specified in another COD entry, given as COD ID. ; loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _cod_enantiomer_of 1234567 ; ; The value of this data item is a COD number (aka COD identifier). The COD record with this COD identifier contains a strcuture of the enantiomeric coompound. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - data_cod_duplicate_[] _name '_cod_duplicate_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _cod_duplicate_entry 2011331 ; ; Example 1 - base on COD entry 1000000.cif, revision 350 svn://www.crystallography.net/cod/cif/1/1000000.cif http://www.crystallography.net/1000000.cif ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in this category are to be used for flagging and managing duplicate entries when they are spotted in COD. ; #------------------------------------------------------------------------------ data_cod_duplicate_entry _name '_cod_duplicate_entry' _category cod_duplicate _type char _list no _definition ; Specifies that the COD entry containing this data item is considered to be a duplicate of another entry. The COD number of this other entry, which is considered to be "primary" entry for the structure, is specified as a value of this tag. As a rule, the "primary" entry should be the most complete and comprehensive structure description in COD. This tag is intended to give hints which entries carry exactely the same information and might be excluded from statistics. Normally, the duplicates are not deposited into COD; if a duplicate is already in the COD collection, however, it can not be simple removed since COD numbers are assigned permanently. Thus, this tag is used to flag such entries when noticed. ; #------------------------------------------------------------------------------- data_cod_data_source_[] _name '_cod_data_source_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _cod_data_source_file bq2131.cif _cod_data_source_block I ; ; Example 1 - base on COD entry 2221282.cif, revision 715 svn://www.crystallography.net/cod/cif/1/2221282.cif http://www.crystallography.net/2221282.cif ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items from this category are used to record and trace sources of information deposited into COD. ; #------------------------------------------------------------------------------ data_cod_data_source_file _name '_cod_data_source_file' _category cod_data_source _type char _list no _definition ; Specifies file name of the file that served as a source of data in this COD entry. The file should be recoded without the path or other URL components, since these components usually have no sence o the recipients system. In Unix parlour, the value recoreded should be a basename of the original file. If the full, permamnent URL or URN is known and recorded, the _cod_data_source_URN or _cod_data_source_URL tags should be used instead. For many data sources, however, the basename contains enough information to locate the original source. For instance, CIFs published in IUCr journals have Coeditor Code as a CIF file name, permitting to identify the original paper where the structure is discussed. Other journals may used original articles DOI as a part of the filename for the supplementary CIF file, which also permits to trace back the original paper. Currently, only one source of data, the file that contained cell constants and atomic coordinates, is recorded, and thus this tag is not placed into a loop. In future, if we decide to record other sources of data (e.g. bibliography sources or sources of experimental information), either new looped tags will be introduced or the _list designator of this tag will be changed to 'both'. The problem with other information is that it often comes from the Web or from other databaseses (e.g. from PubMed), and thus does not have an indicative file name assigned by a data provider. ; #------------------------------------------------------------------------------ data_cod_data_source_block _name '_cod_data_source_block' _category cod_data_source _type char _list no _definition ; Specifies file name of the datablock within the file specified in the cod_data_source_file tag that served as a source of data in this COD entry. Only the data block name following the 'data_' header keyword should be recorded, not the whole data block header; i.e. the value specified here should be 'I', *not* 'data_I', for a data block with the header 'data_I'. Currently, only one source of data, the datablock that contained cell constants and atomic coordinates, is recorded, and thus this tag is not placed into a loop. If the data source file is not a CIF, this tag is irrelevan and may be omited or may contain value '.' (dot). ; #------------------------------------------------------------------------------ data_cod_data_source_MD5_sum _name '_cod_data_source_MD5_sum' _category cod_data_source _type char _list both _definition ; Provides MD5 cryptographic checksum of the source data file that was used to generate this COD entry. If more than one source file was used, the tag may be used in a loop with the corresponding file names. The file from which the checksum was computed should be the same file as mentioned in the corresponding _cod_data_source_file value. ; #------------------------------------------------------------------------------ data_cod_data_source_SHA1_sum _name '_cod_data_source_SHA1_sum' _category cod_data_source _type char _list no _definition ; Provides SHA1 cryptographic checksum of the source data file that was used to generate this COD entry. If more than one source file was used, the tag may be used in a loop with the corresponding file names. The file from which the checksum was computed should be the same file as mentioned in the corresponding _cod_data_source_file value. ; #------------------------------------------------------------------------------ data_cod_data_source_SHA256_sum _name '_cod_data_source_SHA256_sum' _category cod_data_source _type char _list no _definition ; Provides SHA256 cryptographic checksum of the source data file that was used to generate this COD entry. If more than one source file was used, the tag may be used in a loop with the corresponding file names. The file from which the checksum was computed should be the same file as mentioned in the corresponding _cod_data_source_file value. ; #------------------------------------------------------------------------------ data_cod_error_[] _name '_cod_error_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; ... provide error and warning example from COD here ; ; ... provide the COD source reference here ; _definition ; Data from this category flag and describe problems (errors, warnings, etc.) that were discovered in a prticular COD entry during deposition, validation or review. ; #------------------------------------------------------------------------------ data_cod_error_flag _name '_cod_error_flag' _category cod_error _type char _list no loop_ _enumeration _enumeration_detail none 'no errors are detected in this entry (may be omited)' warnings 'some suspicious properties of the data or syntax' errors 'mistakes in the file that make data unusable' retracted 'structure or paper was retracted by authors' _definition ; Describes the severity of errors if such are detected in COD entries: none means that the entry is clean and can be used with confidence; normally the tag with this value can be omitted. warnings data or syntax have suspicious properties, or some missing pieces of information, but the main data items (unit cell, coordinates, chemical formula) should be mostly correct. Warnings may used to indicate internal inconsistencies (e.g. mismatches between declared chemical formula sum and the actual atomic composition), that do not show an obviously incorrect structure; unusual bond geometries, valencies, packing voids, etc. errors the file has serious errors; the data are either wrong or unusable due to dictionary non-conformace, obvious data errors, known experimental errors, missing tags. retracted The original paper describing the structure, or the COD CIF file was retracted by authors. ; #------------------------------------------------------------------------------ data_cod_error_source _name '_cod_error_source' _category cod_error _type char _list no loop_ _enumeration _enumeration_detail deposition ; Problems were inroduced at the stage of structure deposition to COD. The entry should be corrected after consulting the original data source if it is available. ; upstream ; Problems were introduced in the intermediate source (another database, Web site, revire publication, etc.) from which COD obtained data, but the original publication is either not found or is correct. In the latter case, obviously, the problem will be corrected from the original publication, but the errorneous COD entry can be flagged for documentation purposes and commited to the version control repository before correction. ; original ; Problem can be traced back to the original publication. Despite the problem in the publication, there are no indications however that the experiment was performed incorrectly. ; experiment ; Problems were introduced when performing the experiment. ; unknown ; The source of the problem is not known ; _definition ; Describes the most distant (i.e. the closest to the data origin) COD source where the origin of the detected problem (error, warning, etc.) can be traced back. ; #------------------------------------------------------------------------------ data_cod_error_description _name '_cod_error_description' _category cod_error _type char _list no _definition ; Provides a human-readable description of the problems identified in the COD entry bearing the _cod_error_... records. ; #------------------------------------------------------------------------------- data_cod_database_[] _name '_cod_database_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _cod_database_code 2011000 ; ; Example 1 - based on COD entry 2011000.cif, revision 966 svn://www.crystallography.net/cod/cif/1/2011000.cif http://www.crystallography.net/2011000.cif ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items from this category are used for COD bookkeeping records, such as assigned COD number (aka COD database code). ; #------------------------------------------------------------------------------ data_cod_database_code _name '_cod_database_code' _category cod_datatabase _type numb _list no _definition ; Specifies COD number assigned upon deposition into COD to the crystal structure described in the CIF. ; #------------------------------------------------------------------------------ data_cod_database_fobs_code _name '_cod_database_fobs_code' _category cod_datatabase _type numb _list both _definition ; Specifies COD number of the Fobs file. Normally, the same number is assigned in COD for both cordinate and structure factor (aka Fobs) CIF; for powder diffraction experiments, however, one set of difractograms will be assigned one COD number, and all phases refined against them will refer to this single observed data COD number, while each phase will get a distinct COD ID of its own. It may be usual, although not required, that the diffractogram set gets the same COD ID as is assigned to the first phase in the experiment. ; data_cod_database_coordinates_code _name '_cod_database_coordinates_code' _category cod_datatabase _type numb _list both _definition ; Specifies COD number(s) of coordinate files that were determined from this observed datase; to be inserted into COD Fobs (.hkl) files. ; #------------------------------------------------------------------------------ data_cod_depositor_[] _name '_cod_depositor_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; === 2/2000017.cif === _cod_depositor_comments ; The following automatic conversions were performed: '_symmetry_cell_setting' value 'Monoclinic' changed to 'monoclinic' according to '/home/saulius/struct/CIF-dictionaries/cif_core.dic' dictionary named 'cif_core.dic' version 2.4.1 from 2010-06-29. Automatic conversion script Id: cif_fix_enum 1468 2010-11-05 11:02:30Z adriana ; ; ; Example 1 - based on COD entry 2000017.cif, revision 3898 svn://www.crystallography.net/cod/cif/2/2000017.cif http://www.crystallography.net/2000017.cif ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; === 2/2000154.cif === _cod_depositor_comments ; The H-M spacegroup name 'A 1 1 2/a' in the original CIF seems to be wrong, it is incompatible with the 'b axis unique' comment. The b axis unique simbol should be 'A 1 2/a 1'. Encifer shows better packing when H-M symbol is changed to 'A 1 2/a 1' Saulius Gra\