PDBx/mmCIF General FAQ

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class="row"> <h2>PDBx/mmCIF <small>General FAQ</small></h2> </div>  <div class="panel-group" id="accordion"> <div class="panel"> <div class="panel-heading"> <h3 class="panel-title"> <a class="accordion-toggle" data-toggle="collapse" data-parent="#accordion" href="#collapse1"> <span class="glyphicon glyphicon-plus"></span> What should every PDB user know about the PDB format? </a> </h3> </div> <div id="collapse1" class="panel-collapse collapse in"> <div class="panel-body"> <ol class="ul-lg"> <li>PDB entries are distributed in the PDB File Format following the specification described in the <a href="http://wwpdb.org/documentation/file-format" target="_blank">Contents Guide Version 3.30 (Nov. 21, 2012)</a>. The PDB file format is no longer being modified or extended to support new content. </li> <li> Large structures (containing >62 chains and/or 99999 ATOM records) that cannot be fully represented in the PDB File Format are available in the PDB archive as single PDBx/mmCIF files. These large structures are also distributed in “bundled” TAR files containing a collection of best effort/minimal files in the PDB File Format. </li> </ol> </div> </div> </div> <div class="panel"> <div class="panel-heading"> <h3 class="panel-title"> <a class="accordion-toggle" data-toggle="collapse" data-parent="#accordion" href="#collapse4"> <span class="glyphicon glyphicon-plus"></span> What should every PDB user know about PDBx/mmCIF? </a> </h3> </div> <div id="collapse4" class="panel-collapse collapse"> <div class="panel-body"> <ol class="ul-lg"> <li> PDBx/mmCIF became the standard PDB archive format in 2014. </li> <li> All PDB data processing and annotation will be performed using PDBx/mmCIF at all wwPDB sites.</li> <li> PDBx/mmCIF consists of categories of information represented as tables and keyword value pairs.</li> <li> The categories in mmPDBx/mmCIF have explicit relationships with one another. </li> <li> PDBx/mmCIF imposes no limitations for the number of atoms, residues or chains that can be represented in a single PDB entry (no split entries!).</li> <li> Each data item in a PDBx/mmCIF file is precisely defined in a <a href="/dictionaries/mmcif_pdbx_v50.dic/Index">PDBx Exchange Data Dictionary</a> The content of data dictionary is fully software accessible.</li> <li> All of the data items in the current PDB format have corresponding items data items in the PDBx/mmCIF format. </li> <li> Chemical descriptions of all of the monomers and ligands in PDB entries are provided in the PDB Chemical Component Dictionary which is in PDBx/mmCIF format.</li> <li> PDBx/mmCIF is supported by visualization applications such as Jmol, Chimera, and OpenRasMol as well as structure determination systems such as CCP4 and Phenix. </li> </ol> </div> </div> </div>  <div class="panel"> <div class="panel-heading"> <h4 class="panel-title"> <a class="accordion-toggle" data-toggle="collapse" data-parent="#accordion" href="#collapse2"> <span class="glyphicon glyphicon-plus"></span> What should every programmer know about PDBx/mmCIF? </a> </h4> </div> <div id="collapse2" class="panel-collapse collapse"> <div class="panel-body"> <ol class="ul-lg"> <li> The format is based on a context-free grammar. PDBx/mmCIF has a simple grammar. Data are presented in either key-value or tabular form. It is much easier to parse than the record-oriented PDB format. Say good-bye to "exception" handling when reading old-style PDB flat files!</li> <li> There are no column width limitations.</li> <li> All relationships between common data items (e.g. atom and residue identifiers) are explicitly documented within the <a href="/dictionaries/mmcif_pdbx_v50.dic/Index/">PDBx Exchange Dictionary</a>. This permits software applications to evaluate and validate referential integrity with any PDB entry.</li> <li> The mmCIF/PDBx Exchange Dictionary provides metadata (e.g. data types, allowed ranges, controlled vocabularies) which can be used to generate a validating mmCIF parser or a database loader.</li> <li> Parsing tools are available in most popular languages (e.g. C/C++, Java, Python, Perl, FORTRAN) and toolkits (e.g. BioJava and BioPython).</li> <li> Mapping information between the residue sequences of the experimental sample and the model coordinates is included within each entry.</li> <li> PDB Chemical reference data are maintained and distributed in PDBx/mmCIF format.</li> </ol> </div> </div> </div>  <div class="panel"> <div class="panel-heading"> <h4 class="panel-title"> <a class="accordion-toggle" data-toggle="collapse" data-parent="#accordion" href="#collapse3"> <span class="glyphicon glyphicon-plus"></span> What are the format styling plans for PDBx/mmCIF? </a> </h4> </div> <div id="collapse3" class="panel-collapse collapse"> <div class="panel-body"> <h5>Plans for a more PDB friendly mmCIF/PDBx ATOM records</h5> <ul class="ul-lg"> <li>All records on a single text line </li> <li>Columns presented in standard column order. </li> <li>Tabular presentation with leading record names (e.g. ATOM, CELL, REFINE) </li> <li>Method independent features in left-most columns (e.g. identifiers & coordinates) </li> <li>Method specific features in the right-most columns (e.g. ADPs, NMR order/disorder parameters) </li> <li>Continue to support PDB nomenclature semantics (e.g. PDB style chains, residue numbering, and insertion codes) </li> </ul> <p class="pg-lg"> The following examples show the ATOM records from the current PDB format and an example from the <i>proposed stylized</i> PDBx/mmCIF format. In the PDBx/mmCIF example the order of columns places the chain, residue and atom nomencature items in the left-most columns. Data items that depend on the experimental method (e.g. occupancy, B-value ) are placed in columns to the left. All of the items of the atom record in the PDBx/mmCIF format example are placed on a single text line and are white-space delimited. </p> <h5>Example of Record-oriented PDB Format ATOM Records</h5> <div class="highlight"> <div class="my-monospace"> ATOM 1 N GLN A 39 24.690 -27.754 24.275 1.00 60.76 N ATOM 2 CA GLN A 39 23.581 -26.768 24.416 1.00 60.98 C ATOM 3 C GLN A 39 23.990 -25.379 23.905 1.00 59.98 C ATOM 4 O GLN A 39 25.070 -25.209 23.330 1.00 60.25 O ATOM 5 CB GLN A 39 23.136 -26.685 25.878 1.00 60.69 C ATOM 6 N VAL A 40 23.115 -24.395 24.122 1.00 59.58 N ATOM 7 CA VAL A 40 23.342 -23.010 23.690 1.00 57.26 C ATOM 8 C VAL A 40 24.000 -22.152 24.778 1.00 56.00 C ATOM 9 O VAL A 40 23.992 -20.920 24.692 1.00 55.53 O ATOM 10 CB VAL A 40 22.015 -22.337 23.275 1.00 57.32 C </div> </div> <h5>Example of PDBx/mmCIF ATOM Records (atom_site category)</h5> <div class="highlight"> <div class="my-monospace"> loop_ _atom_site.group_PDB _atom_site.id _atom_site.auth_atom_id _atom_site.type_symbol _atom_site.auth_comp_id _atom_site.auth_asym_id _atom_site.auth_seq_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.pdbx_PDB_model_num _atom_site.occupancy _atom_site.pdbx_auth_alt_id _atom_site.B_iso_or_equiv ATOM 1 N N GLN A 39 24.690 -27.754 24.275 1 1.000 . 60.760 ATOM 2 CA C GLN A 39 23.581 -26.768 24.416 1 1.000 . 60.980 ATOM 3 C C GLN A 39 23.990 -25.379 23.905 1 1.000 . 59.980 ATOM 4 O O GLN A 39 25.070 -25.209 23.330 1 1.000 . 60.250 ATOM 5 CB C GLN A 39 23.136 -26.685 25.878 1 1.000 . 60.690 ATOM 6 N N VAL A 40 23.115 -24.395 24.122 1 1.000 . 59.580 ATOM 7 CA C VAL A 40 23.342 -23.010 23.690 1 1.000 . 57.260 ATOM 8 C C VAL A 40 24.000 -22.152 24.778 1 1.000 . 56.000 ATOM 9 O O VAL A 40 23.992 -20.920 24.692 1 1.000 . 55.530 ATOM 10 CB C VAL A 40 22.015 -22.337 23.275 1 1.000 . 57.320 ATOM 11 N N ALA A 41 24.560 -22.804 25.797 1 1.000 . 54.570 </div> </div> </div> </div> </div> <div class="panel">  <div class="panel-heading"> <h4 class="panel-title"> <a class="accordion-toggle" data-toggle="collapse" data-parent="#accordion" href="#faq_f2"> <span class="glyphicon glyphicon-plus"></span> Where can I find the PDBx/mmCIF data files for PDB entries? </a> </h4> </div> <div id="faq_f2" class="panel-collapse collapse"> <div class="panel-body"> <p>PDB entries in PDBx/mmCIF format are stored on the ftp sites of the wwPDB partners at one of the locations:</p> <ul class="ul-lg"> <li><a href="ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/mmCIF/" target="_blank" class="white">ftp for PDBx/mmCIF at RCSB PDB, ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/mmCIF/</a> </li> <li><a href="ftp://ftp.ebi.ac.uk/pub/databases/pdb/data/structures/divided/mmCIF/" class="white" target="_blank">ftp for PDBx/mmCIF at PDBe,ftp://ftp.ebi.ac.uk/pub/databases/pdb/data/structures/divided/mmCIF/</a></li> <li><a href="ftp://ftp.pdbj.org/pub/pdb/data/structures/divided/mmCIF/" class="white" target="_blank">ftp for PDBx/mmCIF at PDBj, ftp://ftp.pdbj.org/pub/pdb/data/structures/divided/mmCIF/</a></li> </ul> <p>Entries containing very large structures stored PDBx/mmCIF format are currently stored separately one of the locations: </p> <ul class="ul-lg"> <li><a href="ftp://ftp.wwpdb.org/pub/pdb/data/large_structures/mmCIF/" target="_blank" class="white">ftp for large PDBx/mmCIF at RCSB PDB, ftp://ftp.wwpdb.org/pub/pdb/data/large_structures/mmCIF/</a> </li> <li><a href="ftp://ftp.ebi.ac.uk/pub/databases/pdb/data/large_structures/mmCIF/" class="white" target="_blank">ftp for large PDBx/mmCIF at PDBe, ftp://ftp.ebi.ac.uk/pub/databases/pdb/data/large_structures/mmCIF/</a></li> <li><a href="ftp://ftp.pdbj.org/pub/pdb/data/large_structures/mmCIF/" class="white" target="_blank">ftp for large PDBx/mmCIF at PDBj, ftp://ftp.pdbj.org/pub/pdb/data/large_structures/mmCIF/</a></li> </ul> <p> The PDBx/mmCIF format files are named following the convention <code><PDB_4-LETTER-ID_CODE>.cif.gz</code> (e.g. 1abc.cif.gz). Experimental data files containing X-ray structure factors are only distributed in PDBx/mmCIF format and are named following an older PDB naming convention <code>r<PDB_ID_CODE>sf.ent.gz</code> (e.g. r1abcsf.ent.gz). </p> <p> A complete description of the download options for PDB data files is maintained at <a href="http://www.wwpdb.org/downloads.html">here</a> by the wwPDB. The special handling of PDB entries containing very large structures is available <a href="/docs/large-pdbx-examples/">here</a>. </p> </div> </div> </div>  <div class="panel">  <div class="panel-heading"> <h3 class="panel-title"> <a class="accordion-toggle" data-toggle="collapse" data-parent="#accordion" href="#faq_f3"> <span class="glyphicon glyphicon-plus"></span> Are PDBx/mmCIF files hard to read? What does the syntax look like? </a> </h3> </div> <div id="faq_f3" class="panel-collapse collapse"> <div class="panel-body"> <p>The PDBx/mmCIF format has a simple appearance with only a few syntax elements. All of syntax elements used in PDBx data files are shown in the following snippet describing polymer sequence. </p> <p> The essential syntax features include:</p> <ul> <li> All data items are identified by name and begin with the underscore character, <code>_entity_poly.entity_id</code>. <li> Data item names can be decomposed into a category name and an attribute name, <code>_category.attribute</code> which are separated by a period. <li> Data categories are presented in two styles: key-value and tabular. In the example, categories <code>entity_name_com</code> and <code>entity_poly</code> both use the key-value style and the <code>entity_poly_seq</code> category uses the tabular style. In the tabular sytle, the data item names correpsonding to the table columns follow a reserved <code>loop_</code> token which are followed by the rows of data rows of white-space delimited data values. <li> Any character data value may be quoted using encapsulating single or double quotes; however, character values containing internal whitespace (e.g. the value of <code>_entity_name_com.name</code>) must be quoted. Character values that extend over multiple lines are quoted using leading and trailing semi-colons positioned at the first character position of the records surronding the multi-line character value (e.g.<code>_entity_poly.pdbx_seq_one_letter_code</code>). <li> Lines beginning with the hash symbol <code>#</code> are comments. </ul> <p> Look <a href="/docs/tutorials/mechanics/pdbx-mmcif-syntax.html">here</a> for a more complete description of PDBx/mmCIF data file and dictionary syntax. </p> <pre> # <-- a comment line _entity_name_com.entity_id 1 _entity_name_com.name "Pantoate--beta-alanine ligase, Pantoate-activating enzyme" _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code ;AMAIPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPMQFGAGGDL DAYPRTPDDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGE KDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVL DAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIGTFAGTDRPDGYR ; # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 ALA n 1 2 MET n 1 3 ALA n 1 4 ILE n 1 5 PRO n 1 6 ALA n 1 7 PHE n # .... abbreviated .... </pre> </div> </div> </div>  <div class="panel">  <div class="panel-heading"> <h3 class="panel-title"> <a class="accordion-toggle" data-toggle="collapse" data-parent="#accordion" href="#faq_f1"> <span class="glyphicon glyphicon-plus"></span> What is the formal syntax specification for PDBx/mmCIF? </a> </h3> </div> <div id="faq_f1" class="panel-collapse collapse"> <div class="panel-body"> The PDBx/mmCIF data files produced by the wwPDB conform to both the CIF 1.0 and 1.1 syntax specifications. The current syntax specification for CIF 1.1 is maintained at the <a href="http://www.iucr.org/resources/cif/spec/version1.1/cifsyntax">IUCr CIF site</a>. </div> </div> </div>  <div class="panel">  <div class="panel-heading"> <h3 class="panel-title"> <a class="accordion-toggle" data-toggle="collapse" data-parent="#accordion" href="#faq_w1"> <span class="glyphicon glyphicon-plus"></span> Can line-base editing tools like <i>grep</i> and <i>awk</i> be used on PDBx/mmCIF files? </a> </h3> </div> <div id="faq_w1" class="panel-collapse collapse"> <div class="panel-body"> <p> Yes, the atom coordindate records in the PDBx/mmCIF data distributed by the wwPDB are stored on individual lines each beginning with either 'ATOM' or 'HETATM'. The elements of each coordinate record are white-space delimited. For example, PDBx/mmCIF coordinate records in PDB entries all have the following regular layout. </p> <pre> loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.Cartn_x_esd _atom_site.Cartn_y_esd _atom_site.Cartn_z_esd _atom_site.occupancy_esd _atom_site.B_iso_or_equiv_esd _atom_site.pdbx_formal_charge _atom_site.auth_seq_id _atom_site.auth_comp_id _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.pdbx_PDB_model_num ATOM 1 N N . VAL A 1 1 ? 6.204 16.869 4.854 1.00 49.05 ? ? ? ? ? ? 1 VAL A N 1 ATOM 2 C CA . VAL A 1 1 ? 6.913 17.759 4.607 1.00 43.14 ? ? ? ? ? ? 1 VAL A CA 1 ATOM 3 C C . VAL A 1 1 ? 8.504 17.378 4.797 1.00 24.80 ? ? ? ? ? ? 1 VAL A C 1 ATOM 4 O O . VAL A 1 1 ? 8.805 17.011 5.943 1.00 37.68 ? ? ? ? ? ? 1 VAL A O 1 ATOM 5 C CB . VAL A 1 1 ? 6.369 19.044 5.810 1.00 72.12 ? ? ? ? ? ? 1 VAL A CB 1 ATOM 6 C CG1 . VAL A 1 1 ? 7.009 20.127 5.418 1.00 61.79 ? ? ? ? ? ? 1 VAL A CG1 1 ATOM 7 C CG2 . VAL A 1 1 ? 5.246 18.533 5.681 1.00 80.12 ? ? ? ? ? ? 1 VAL A CG2 1 ATOM 8 N N . LEU A 1 2 ? 9.096 18.040 3.857 1.00 26.44 ? ? ? ? ? ? 2 LEU A N 1 ATOM 9 C CA . LEU A 1 2 ? 10.600 17.889 4.283 1.00 26.32 ? ? ? ? ? ? 2 LEU A CA 1 ATOM 10 C C . LEU A 1 2 ? 11.265 19.184 5.297 1.00 32.96 ? ? ? ? ? ? 2 LEU A C 1 ATOM 11 O O . LEU A 1 2 ? 10.813 20.177 4.647 1.00 31.90 ? ? ? ? ? ? 2 LEU A O 1 ATOM 12 C CB . LEU A 1 2 ? 11.099 18.007 2.815 1.00 29.23 ? ? ? ? ? ? 2 LEU A CB 1 ATOM 13 C CG . LEU A 1 2 ? 11.322 16.956 1.934 1.00 37.71 ? ? ? ? ? ? 2 LEU A CG 1 ATOM 14 C CD1 . LEU A 1 2 ? 11.468 15.596 2.337 1.00 39.10 ? ? ? ? ? ? 2 LEU A CD1 1 ATOM 15 C CD2 . LEU A 1 2 ? 11.423 17.268 0.300 1.00 37.47 ? ? ? ? ? ? 2 LEU A CD2 1 </pre> <p> The following command will extract the PDB atom record name, atom name, residue name, chain identifier, residue number, Cartesian X, Y, and Z coordinates from the above snippet of PDBx/mmCIF coordinate data for PDB entry 4HHB. </p> <pre> grep '^ATOM' 4HHB.cif | awk '{print $1, $25, $23, $24, $22, $11, $12, $13}' </pre> </div> </div> </div>  <div class="panel">  <div class="panel-heading"> <h3 class="panel-title"> <a class="accordion-toggle" data-toggle="collapse" data-parent="#accordion" href="#faq_w2"> <span class="glyphicon glyphicon-plus"></span>How are the atom records described in PDBx/mmCIF? </a> </h3> </div> <div id="faq_w2" class="panel-collapse collapse"> <div class="panel-body"> Coordinate data is recorded in PDBx/mmCIF <a href="/dictionaries/mmcif_pdbx_v50.dic/Categories/atom_site.html">ATOM_SITE</a> data category. This <a href="/docs/tutorials/content/atomic-description.html">brief tutorial</a> describes the PDBx/mmCIF representation of coordinated data and the relationship to PDB format coodinate data items. </div> </div> </div>  <div class="panel">  <div class="panel-heading"> <h3 class="panel-title"> <a class="accordion-toggle" data-toggle="collapse" data-parent="#accordion" href="#faq_w3"> <span class="glyphicon glyphicon-plus"></span>How are macromolecules described in PDBx/mmCIF? </a> </h3> </div> <div id="faq_w3" class="panel-collapse collapse"> <div class="panel-body"> This <a href="/docs/tutorials/content/molecular-entities.html">brief tutorial</a> describes the PDBx/mmCIF representation of polymer and non-polymer molecular entities. </div> </div> </div>  <div class="panel">  <div class="panel-heading"> <h3 class="panel-title"> <a class="accordion-toggle" data-toggle="collapse" data-parent="#accordion" href="#faq_w4"> <span class="glyphicon glyphicon-plus"></span>What data categories are used in the Chemical Component Dictionary? </a> </h3> </div> <div id="faq_w4" class="panel-collapse collapse"> <div class="panel-body"> The collection of PDBx/mmCIF data categories used in the Chemical Component Dictionary are in the <a href="/dictionaries/mmcif_pdbx_v50.dic/Groups/chem_comp_dictionary_group.html">CHEM_COMP_DICTIONARY</a> category group. </div> </div> </div>  <div class="panel">  <div class="panel-heading"> <h3 class="panel-title"> <a class="accordion-toggle" data-toggle="collapse" data-parent="#accordion" href="#faq_w5"> <span class="glyphicon glyphicon-plus"></span>What data categories are used in the Biologically Interesting molecule Reference Dictionary (BIRD)? </a> </h3> </div> <div id="faq_w5" class="panel-collapse collapse"> <div class="panel-body"> The collection of PDBx/mmCIF data categories and items used in the Biologically Interesting molecule Reference Dictionary (BIRD) are in the <a href="/dictionaries/mmcif_pdbx_v50.dic/Groups/bird_dictionary_group.html">BIRD_DICTIONARY</a> category group. </div> </div> </div>  </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>

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