PDBx/mmCIF Glossary

<!DOCTYPE html> <html lang="en"> <head>  <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <link href="/assets/css/bootstrap/css/bootstrap.css" rel="stylesheet">  <link href="/styles/app.css" rel="stylesheet"> <link href="/styles/prettify.css" rel="stylesheet">   <link href="/assets/webfonts/LeagueGothic/stylesheet.css" rel="stylesheet">  <link href="/assets/webfonts/Titillium/fonts.css" rel="stylesheet">  <link href="/assets/webfonts/Colaborate/colaborate_thin_macroman/stylesheet.css" rel="stylesheet">  <link href="/assets/webfonts/DroidSans/droidsans_regular_macroman/stylesheet.css" rel="stylesheet">  <link href="/assets/webfonts/Existence/existence_light_macroman/stylesheet.css" rel="stylesheet">  <link href="/assets/webfonts/Existence/existence_stencillight_macroman/stylesheet.css" rel="stylesheet">  <link href="/assets/webfonts/Existence/existence_unicaselight_macroman/stylesheet.css" rel="stylesheet">  <link href="/assets/webfonts/Roboto/roboto_thin_macroman/stylesheet.css" rel="stylesheet">  <link href="/assets/webfonts/Roboto/roboto_light_macroman/stylesheet.css" rel="stylesheet">    <title>PDBx/mmCIF Glossary</title> </head> <body> <div id="wrap">   <div class="navbar navbar-inverse navbar-fixed-top"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".nav-collapse"> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <a class="my-navbar-brand" href="/pdbx-mmcif-home-page.html">PDBx/mmCIF</a> </div>  <div class="collapse navbar-collapse"> <ul class="nav navbar-nav">  <li><a href="/pdbx-mmcif-home-page.html">Home</a></li>  <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown">Dictionaries<b class="caret"></b></a> <ul class="dropdown-menu"> <li class="divider"></li> <li class="dropdown-header">Browse the PDBx/mmCIF Dictionaries</li> <li><a href="/dictionaries/mmcif_pdbx_v50.dic/Index">Current version (V5) PDBx/mmCIF</a></li> <li><a href="/dictionaries/mmcif_pdbx_v5_next.dic/Index">Development Version PDBx/mmCIF</a></li> <li><a href="/dictionaries/mmcif_ddl.dic/Index">Dictionary Definition Language V2</a></li> <li><a href="/dictionaries/mmcif_pdbx_vrpt.dic/Index">wwPDB Validation</a></li> <li class="divider"></li> <li class="dropdown-header">Browse Other Dictionaries</li> <li><a href="/dictionaries/mmcif_ihm_ext.dic/Index">IHMCIF</a></li> <li><a href="/dictionaries/mmcif_ihm_flr_ext.dic/Index">flrCIF</a></li> <li><a href="/dictionaries/mmcif_pdbx_v40.dic/Index">Previous PDBx/mmCIF V4</a></li> <li><a href="/dictionaries/mmcif_std.dic/Index">Original mmCIF</a></li> <li><a href="/dictionaries/mmcif_nmr-star.dic/Index">NMRIF/NMR-STAR</a></li> <li><a href="/dictionaries/mmcif_nef.dic/Index">NMR Exchange Format (NEF)</a></li> <li><a href="/dictionaries/mmcif_sas.dic/Index">SAS</a></li> <li><a href="/dictionaries/mmcif_ndb_ntc.dic/Index">NDB NTC</a></li> <li><a href="/dictionaries/mmcif_em.dic/Index">3DEM</a></li> <li><a href="/dictionaries/mmcif_img.dic/Index">Image mmCIF</a></li> <li><a href="/dictionaries/mmcif_sym.dic/Index">Symmetry</a></li> <li><a href="/dictionaries/mmcif_biosync.dic/Index">Biosync</a></li> <li><a href="/dictionaries/mmcif_ma.dic/Index">ModelCIF</a></li> </ul> </li>  <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown">Documentation<b class="caret"></b></a> <ul class="dropdown-menu"> <li class="divider"></li> <li><a href="/docs/faqs/pdbx-mmcif-faq-general.html">PDBx/mmCIF FAQ</a></li> <li><a href="/docs/user-guide/guide.html">PDBx/mmCIF User Guide</a></li> <li class="divider"></li> <li class="dropdown-header">Format</li> <li><a href="/docs/large-pdbx-examples/index.html">Large Structures in PDBx/mmCIF</a></li> <li><a href="/docs/pdb_to_pdbx_correspondences.html">PDB to PDBx Format Correspondences</a></li> <li><a href="http://wwpdb.org/task/mmcif" target="_blank">wwPDB PDBx/mmCIF Working Group</a></li> <li class="divider"></li> <li class="dropdown-header">Software</li> <li><a href="/docs/software-resources.html">Software resources</a></li> <li><a href="/docs/sw-examples/cpp/html">C++ Examples</a></li> <li><a href="/docs/sw-examples/python/html">Python Examples</a></li> <li class="divider"></li> <li class="dropdown-header">Reference</li> <li><a href="/docs/tutorials/mechanics/pdbx-mmcif-syntax.html">File syntax</a> </li> <li> <a href="/docs/tutorials/mechanics/pdbx-mmcif-dict-struct.html">Dictionary organization</a></li> <li><a href="/docs/tutorials/content/atomic-description.html">Atomic description</a></li> <li><a href="/docs/tutorials/content/molecular-entities.html">Molecular description</li> <li><a href="/docs/pubs/pdbx-mmcif-references.html">Reference List</a></li> <li><a href="/docs/tutorials/glossary/early-history.html">Early history</a></li> <li><a href="/docs/tutorials/glossary/pdbx-mmcif-glossary.html">Glossary</a></li> </ul> </li> <li><a href="/dictionaries/downloads.html">Downloads</a></li> <li><a href="mailto:pdbx-mmcif-help@mail.wwpdb.org">Contact Us</a></li> </ul>  <a href="http://www.wwpdb.org/" class="pull-right right-icon" title="Worldwide Protein Data Bank"> <img alt="A Member of the wwPDB" src="/assets/images/wwpdb/wwpdb-logo-menubar-20.png" width="107" height="20"></a> <form class="navbar-form pull-right" id="searchSite" action="/cgi-bin/swish/swish.cgi" method="get" enctype="application/x-www-form-urlencoded"> <button type="submit" class="btn btn-wwpdb-green"> <span class="glyphicon glyphicon-search"></span></a> </button> <div class="form-group"> <input type="text" placeholder="Search current dictionary" class="form-control" size=25 name="query"> </div> <input type="hidden" name="sort" value="swishrank" /> <input type="hidden" name="si" value="0" /> </form>  </div> </div>  </div>    <div class="container"> <div class="row"> <h2>PDBx/mmCIF Glossary</h2> </div> <div class="row"> <DL class="dl-horizontal dl-lg"> <a name="A-M"></a> <DT>attribute <DD> A column or field in a table. The term attribute is often used as a synonym for an mmCIF data item name. <DT>category <DD> Collections of related data items are organized in mmCIF categories. A category is a tabular data structure. Within a category, those data items that determine the uniqueness of each row in the category/table are designated as key data items of the category. <DT>category group <DD> A category group is a named collection of categories. Categories groups are typically used to organize groups of related categories. For instance, all of the mmCIF categories containing bibliographic information are members of CITATION_GROUP category group. <DT>CIF <DD> Crystallographic Information Framework <DT>data block <DD> A data block is an element of STAR grammar. A data block begins with the token data_ and is terminated by another data_ token or the end of file. Data blocks are named by appending a text string to the data_ token. In mmCIF data files and dictionaries data blocks are used as named logical partitions. Each data block within a file is logically independent and defines an independent scope. Data blocks may not be nested within mmCIF files. <DT>data item <DD> Item and item name refer to the name of an individual element of data. For instance, _atom_site.Cartn_X refers to the x Cartesian coordinate. mmCIF item names all begin with an underscore character. This is a convention of the STAR grammar. The remainder of the item consists of a category name and an item keyword separated by a period. The mmCIF item keyword is the unique identifier for the item within its category (mmCIF synonyms: item, item name, and data item name). <DT>data file <DD> Although mmCIF uses a uniform syntax based on STAR for expressing files containing dictionaries and data, there are some differences in these files which require distinction. The term data file is reserved for files which contain only collections of data items and values. On the hand, mmCIF dictionaries contain primarily definitions encoded in save frames. Save frames may appear only in mmCIF dictionaries. <DT>data type <DD> mmCIF uses regular expressions to define the patterns which must be matched by each data value. The mmCIF dictionary contains a list of the regular expressions describing each data type in the category ITEM_TYPE_LIST. Each mmCIF definition contains a reference to one of these regular expressions. <DT>DDL <DD> DDL is an acronym for Dictionary Definition Language. The role of DDL is to define the components (data items) from which definitions may be constructed. DDL2 provides the framework on which the mmCIF dictionary is based. <DT>domain <DD> The pool of legal values that may be assigned to a data item. <DT>enumeration <DD> A list of allowed values. An mmCIF definition may include the list of discrete values that are permitted for a particular data item. For example, the mmCIF definition for the method used to produce a chemical entity (_entity.src_method) can have three values: <i>man</i> for a genetically manipulated source, <i>nat</i> for a material from a natural source, <i>syn</i> for synthetic source. <DT>item value <DD> The value assigned to an mmCIF data item. The simplest form of the STAR grammar consists of pairs of data items and data values. <DT>key or key item <DD> The unique identifier for each row in an mmCIF category. <DT>loop <DD> A loop is an element of the STAR grammar. In order to encode a vector or table of data, an individual data item or a group of data items within the same category may be preceded by a loop_ token. The list of data item names can then be followed by repeated rows of data values. The number of data values must be an exact multiple of the number of data items. CIF and mmCIF do not permit the nesting of loops. The following example builds a small table of atomic positions. <pre> loop_ _atom_site.type_symbol _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.id N 25.369 30.691 11.795 1 C 25.970 31.965 12.332 2 C 25.569 32.010 13.808 3 O 24.735 31.190 14.167 4 </pre> <DT>mandatory data item <DD> A mandatory data item must appear in any instance of the category to which the item belongs. Data items which are category keys are always mandatory data items. Other items may be defined as mandatory when their presence is required for each row of the category to have a meaningful interpretation. For instance, in the ATOM_SITE category, the item _atom_site.type_symbol is a reference to the elemental symbol, and is defined as mandatory. <DT>mmCIF <DD> macromolecular Crystallographic Information Framework <a name="N-Z"></a> <DT>parent-child relationship <DD> A data item which occurs in multiple categories creates a parent-child relationship. In the mmCIF dictionary this most commonly occurs for for labels and identifiers which are reused throughout the dictionary. For instance, the entity identifier _entity.id defined in category ENTITY is the parent definition of this item. This identifier is reused in the ATOM_SITE category as item _atom_site.label_entity_id. In this case, the data item in the ATOM_SITE category is defined as a child of the data item in the ENTITY category. <DT>relation <DD> A table is an informal equivalent of a relation. It is similarly equivalent to an mmCIF category. <DT>regular expression <DD> Regular sets and expressions derive from a very formal decomposition of language structure. In the mmCIF dictionary, a regular expression notation is used to define the patterns which must be matched by values of a data item. For instance, a calendar date in the mmCIF dictionary must match a pattern like yyyy-mm-dd, which can be defined by the regular expression [0-9][0-9][0-9][0-9]-[0-9][0-9]-[0-9][0-9]. <DT>save frame <DD> A save frame is a STAR syntax element. A save frame begins with the token save_ and is terminated by another save_ token. Save frames are named by appending a text string to the save_ token. In mmCIF dictionaries save frames are used to encapsulate item and category definitions. The mmCIF dictionary is composed of a data block containing thousands of save frames, where each save frame contains a different definition. Save frames may only appear in mmCIF dictionaries and may not be nested. <DT>scope <DD> A scope delimits logically independent sections. The scope delimiters in the STAR grammar are data blocks and the save frames. Multiple data blocks may occur within a single file, but the definitions and declarations in different data blocks are logically independent. Similarly, save frames delimit sections of independent scope within a data block. The mmCIF dictionary is organized as a collection of save frames within a single data block. Each save frame holds a different definition, and this set of related definitions is arranged in a single data block. <DT>STAR <DD> STAR is the acronym for Self-Defining Text Archive and Retrieval. The syntax used by CIF and mmCIF is derived from the STAR grammar. <DT>subcategory <DD> A subcategory is a named collection of data items within a category. Subcategories are used to indicate a special subsets of data items. For instance, the data items _atom_site.Cartn_x, _atom_site.Cartn_y, and _atom_site.Cartn_z belong to a subcategory named cartesian_coordinate. <DT>table <DD> A table is data structure composed of columns and rows. mmCIF categories are table-like structures in which the data items form the columns and with the data values occupying the rows. <DT>tuple <DD> A tuple is informally equivalent to a row in a table or a row in an mmCIF category. </DL> </div> </div>  </div>   <script src="/assets/js/jquery/core/jquery-1.11.0.min.js" ></script> <script src="/assets/css/bootstrap/js/bootstrap.js" > </script>  <script src="/js/MyApp.js"></script>   <div id="footer"> <div class="container"> <p class="muted credit">© wwPDB </p> </div> </div>  </body> </html>

CINXE.COM

PDBx/mmCIF Glossary