############################################################################### # Model Database Dictionary # # # # Alexei Adzhubei and Eugenia Migliavacca # # GlaxoSmithKline, Geneva # # # # Version 1.0.00, 01/03/1999 # # # # The MDB dictionary is a CIF-based dictionary designed to be used in # # conjunction with the full mmCIF dictionary. # # # # Please email comments to Alexei Adzhubei at aaa75196@gsk.com # # # ############################################################################### # _datablock.id mdb.dic # _datablock.description #; This datablock holds the MDB dictionary version mdb.1.0.00 #; _dictionary.title cif_mdb.dic _dictionary.version 1.0.00 _dictionary.datablock_id cif_mdb.dic ######################### ## CATEGORY_GROUP_LIST ## ######################### loop_ _category_group_list.id _category_group_list.parent_id _category_group_list.description 'inclusive_group' 'inclusive_group' ; Categories that belong to the macromolecular dictionary. ; 'mdb_group' 'inclusive_group' ; Categories that do not belong to the mmCIF dictionary: MDB subset. ; 'mdb_deposition_group' 'mdb_group' ; Categories that contain details about deposition. ; 'mdb_model_group' 'mdb_group' ; Categories that describe model definition and building procedure. ; 'mdb_align_group' 'mdb_group' ; Categories that describe alignments and templates. ; 'mdb_calc_group' 'mdb_group' ; Categories that describe calculation details of the modelling. ; 'mdb_model_struct_group' 'mdb_group' ; Categories that contain details about model structures and model evaluation. ; 'mdb_swp_group' 'mdb_group' ; Categories that guarantee full compatibility with Swiss Prot. ; 'mpw_group' 'mdb_group' ; Categories that do not belong to the mmCIF dictionary: MPW subset. ; save__entity.id _item_description.description ; The value of _entity.id must uniquely identify a record in the ENTITY list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_entity.id' entity yes '_mdb_entity_name_swp.entity_id' mdb_entity_name_swp yes '_mdb_entity_seq_cd.entity_id' mdb_entity_seq_cd yes '_mdb_entity_seq_mon.entity_id' mdb_entity_seq_mon yes '_mdb_entity_seq_relate.entity_id' mdb_entity_seq_relate yes '_mdb_entity_seq_motif.entity_id' mdb_entity_seq_motif yes '_mdb_model.entity_id' mdb_model yes '_mdb_align_search_param.entity_id' mdb_align_search_param no '_mdb_align_thread_param.entity_id' mdb_align_thread_param no '_mdb_align_templates.entity_id' mdb_align_templates no '_mdb_multalign.entity_id' mdb_multalign no '_mdb_multalign_matrix.entity_id' mdb_multalign_matrix no '_mdb_model_proc_seg.entity_id' mdb_model_proc_seg no '_mdb_energy_min.entity_id' mdb_energy_min no '_mdb_dynamics.entity_id' mdb_dynamics no '_mdb_model_struct.entity_id' mdb_model_struct no '_mdb_model_struct_src.entity_id' mdb_model_struct_src no '_mdb_model_struct_ss.entity_id' mdb_model_struct_ss no '_mdb_model_struct_asa.entity_id' mdb_model_struct_asa no '_mdb_model_struct_fold.entity_id' mdb_model_struct_fold no '_mdb_model_eval.entity_id' mdb_model_eval no '_mdb_solved_structure.entity_id' mdb_solved_structure no '_mdb_swp_data.entity_id' mdb_swp_data yes _item_type.code code loop_ _item_linked.child_name _item_linked.parent_name '_mdb_entity_name_swp.entity_id' '_entity.id' '_mdb_entity_seq_cd.entity_id' '_entity.id' '_mdb_entity_seq_mon.entity_id' '_entity.id' '_mdb_entity_seq_relate.entity_id' '_entity.id' '_mdb_entity_seq_motif.entity_id' '_entity.id' '_mdb_model.entity_id' '_entity.id' '_mdb_align_search_param.entity_id' '_entity.id' '_mdb_align_thread_param.entity_id' '_entity.id' '_mdb_align_templates.entity_id' '_entity.id' '_mdb_multalign.entity_id' '_entity.id' '_mdb_multalign_matrix.entity_id' '_entity.id' '_mdb_model_proc_seg.entity_id' '_entity.id' '_mdb_energy_min.entity_id' '_entity.id' '_mdb_dynamics.entity_id' '_entity.id' '_mdb_model_struct.entity_id' '_entity.id' '_mdb_model_struct_src.entity_id' '_entity.id' '_mdb_model_struct_ss.entity_id' '_entity.id' '_mdb_model_struct_asa.entity_id' '_entity.id' '_mdb_model_struct_fold.entity_id' '_entity.id' '_mdb_model_eval.entity_id' '_entity.id' '_mdb_solved_structure.entity_id' '_entity.id' '_mdb_swp_data.entity_id' '_entity.id' save_ save__entity_poly_seq.num _item_description.description ; The value of _entity_poly_seq.num must uniquely and sequentially identify a record in the ENTITY_POLY_SEQ list. Note that this item must be a number, and that the sequence numbers must progress in increasing numerical order. ; loop_ _item.name _item.category_id _item.mandatory_code '_entity_poly_seq.num' entity_poly_seq yes '_mdb_entity_seq_motif.beg_mon_num' mdb_entity_seq_motif yes '_mdb_entity_seq_motif.end_mon_num' mdb_entity_seq_motif yes '_mdb_model_struct.entity_mon_num' mdb_model_struct yes _item_type.code int loop_ _item_linked.child_name _item_linked.parent_name '_mdb_entity_seq_motif.beg_mon_num' '_entity_poly_seq.num' '_mdb_entity_seq_motif.end_mon_num' '_entity_poly_seq.num' '_mdb_model_struct.entity_mon_num' '_entity_poly_seq.num' save_ save__chem_comp.id _item_description.description ; The value of _chem_comp.id must uniquely identify each item in the CHEM_COMP list. For protein polymer entities, this is the three-letter code for amino acids. For nucleic acid polymer entities, this is the one-letter code for the bases. ; loop_ _item.name _item.category_id _item.mandatory_code '_chem_comp.id' chem_comp yes '_mdb_model_struct.mon_id' mdb_model_struct yes _item_type.code ucode loop_ _item_linked.child_name _item_linked.parent_name '_mdb_model_struct.mon_id' '_chem_comp.id' save_ #################### ## MDB_SUBMISSION ## #################### save_MDB_SUBMISSION _category.description ; The category mdb_submission serves to bind entry_id for each model submission to an integer key used to identify separate submissions (entries) in the data stored in other categories. The category also stores flat CIF file location for each entry. ; _category.id mdb_submission _category.mandatory_code yes _category_key.name '_mdb_submission.entry_id' loop_ _category_group.id 'inclusive_group' 'mdb_group' 'mdb_deposition_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; loop_ ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__mdb_submission.entry_id _item_description.description ; This item is a pointer to _entry.id in the category entry. ; _item.name '_mdb_submission.entry_id' _item.category_id mdb_submission _item.mandatory_code yes _item_type.code code save_ save__mdb_submission.file_spec _item_description.description ; This item holds CIF flat file location for entry_id. ; _item.name '_mdb_submission.file_spec' _item.category_id mdb_submission _item.mandatory_code yes _item_type.code line # implemented as bfile in oracle 04.07.00 save_ #################### ## MDB_DEPOSITION ## #################### save_MDB_DEPOSITION _category.description ; Data items in the MDB_DEPOSITION category record details about deposition source. ; _category.id mdb_deposition _category.mandatory_code yes _category_key.name '_mdb_deposition.entry_id' loop_ _category_group.id 'inclusive_group' 'mdb_group' 'mdb_deposition_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; loop_ ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__mdb_deposition.entry_id _item_description.description ; This data is a pointer to _entry.id in the ENTRY category. ; _item.name '_mdb_deposition.entry_id' _item.category_id mdb_deposition _item.mandatory_code yes _item_type.code code save_ save__mdb_deposition.src _item_description.description ; Flag indicating external (ext) or internal (int) deposition. ; _item.name '_mdb_deposition.src' _item.category_id mdb_deposition _item.mandatory_code yes _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail ext 'external deposition' int 'internal deposition' save_ # modification # Alexei -- 04/07/00 # removed _item_default.value ext save__mdb_deposition.auto _item_description.description ; Flag indicating automatic deposition. ; _item.name '_mdb_deposition.auto' _item.category_id mdb_deposition _item.mandatory_code yes _item_type.code uchar1 _item_default.value no loop_ _item_enumeration.value _item_enumeration.detail y 'abbreviation for "yes"' n 'abbreviation for "no"' save_ # modification Alexei -- 21/09/00 # removed # _item_enumeration.value yes # _item_enumeration.value no # changed from # _item_type.code ucode # to # _item_type.code uchar1 save__mdb_deposition.db _item_description.description ; Flag indicating to which database the entry belongs. This item is a child of _mdb_db_list.db_id. ; _item.name '_mdb_deposition.db' _item.category_id mdb_deposition _item.mandatory_code yes _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail asd 'active site database' mdb 'model database' pdb 'protein database' asdm 'active site database models' save_ # modification Alexei - 10/01/01 # added enumeration value asdm # Alexei 16/01/01 changed "_item_type.code uchar3" to "code" # assign VARCHAR2(5) to _mdb_deposition.db in the DB save__mdb_deposition.title _item_description.description ; Short description of the source or origin of the entry. ; _item.name '_mdb_deposition.title' _item.category_id mdb_deposition _item.mandatory_code no _item_type.code text _item_examples.case 'SWISS-MODEL (Automated Protein Modelling Server)' save_ # Alexei -- 21/09/00 # for data loading with the mdbLoader the following conventions are implemented # mdb_deposition.title holds "headers+remarks" or "full data" # to indicate data completeness for mdb_audit.revision_level 0 and higher #save__mdb_deposition.software_name # _item_description.description #; Name of the software used to load entry. #; # _item.name '_mdb_deposition.software_name' # _item.category_id mdb_deposition # _item.mandatory_code no # _item_type.code line # _item_examples.case 'mdbloaderv013.pl' # save_ # _mdb_deposition.software_name added 04.07.00 -- em96794 # Alexei 19/01/01 -- .software_name moved to category mdb_audit # to allow multiple data per entry id ######################### ## MDB_ENTITY_NAME_SWP ## different table: mdb_swp_data ######################### #save_MDB_ENTITY_NAME_SWP # _category.description #; Data items in MDB_ENTITY_NAME_SWP category enforce direct # compatibility with Swiss-Prot Database. #; # _category.id mdb_entity_name_swp # _category.mandatory_code no # _category_key.name '_mdb_entity_name_swp.entity_id' # loop_ # _category_group.id 'inclusive_group' # 'mdb_group' # 'entity_group' # loop_ # _category_examples.detail # _category_examples.case ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #; # Example 1 - # #; #; # loop_ # # #; ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # save_ #save__mdb_entity_name_swp.entity_id # _item_description.description #; This data item is a pointer to _entity.id in the ENTITY # category. #; # _item.name '_mdb_entity_name_swp.entity_id' # _item.category_id mdb_entity_name_swp # _item.mandatory_code yes # _item_type.code code # save_ #save__mdb_entity_name_swp.id # _item_description.description # Identification code (entry name) in Swiss-Prot database. #; # _item.name '_mdb_entity_name_swp.id' # _item.category_id mdb_entity_name_swp # _item.mandatory_code no # _item_type.code ucode # loop_ # _item_examples.case KPBG_RABIT # KGPA_BOVIN # save_ #save__mdb_entity_name_swp.ac # _item_description.description #; Primary accession number in Swiss-Prot database. #; # _item.name '_mdb_entity_name_swp.ac' # _item.category_id mdb_entity_name_swp # _item.mandatory_code yes # _item_type.code ucode # loop_ # _item_examples.case P00518 # P00516 # save_ #save__mdb_entity_name_swp.de # _item_description.description #; Short description as in Swiss-Prot database. #; # _item.name '_mdb_entity_name_swp.de' # _item.category_id mdb_entity_name_swp # _item.mandatory_code no # _item_type.code text # _item_examples.case #; CGMP-DEPENDENT PROTEIN KINASE, ALPHA ISOZYME (CGK) # (EC 2.7.1.37) #; # save_ #save__mdb_entity_name_swp.creation_date # _item_description.description #; Creation date of the entry in Swiss-Prot database. #; # _item.name '_mdb_entity_name_swp.date' # _item.category_id mdb_entity_name_swp # _item.mandatory_code no # _item_type.code yyyy-mm-dd # loop_ # _item_examples.case 1998-12-24 # 1996-01-06 # save_ ####################### ## MDB_ENTITY_SEQ_CD ## ####################### save__MDB_ENTITY_SEQ_CD _category.description ; Data items in the category MDB_ENTITY_SEQ_CD record details about the codon sequence such as reference to the original gene, the database containing the sequence, the identification code, the accession code and the URL of the database. ; _category.id mdb_entity_seq_cd _category.mandatory_code no _category_key.name '_mdb_entity_seq_cd.entity_id' loop_ _category_group.id 'inclusive_group' 'mdb_group' 'entity_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; loop_ ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__mdb_entity_seq_cd.data_scr _item_description.description ; Flag to indicate if the codon sequence was submitted by the author(s) or genereted by MDB. ; _item.name '_mdb_entity_seq_cd.data_scr' _item.category_id mdb_entity_seq_cd _item.mandatory_code yes _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail SD 'submitted data' GD 'generated data' save_ save__mdb_entity_seq_cd.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_mdb_entity_seq_cd.entity_id' _item.category_id mdb_entity_seq_cd _item.mandatory_code yes _item_type.code code save_ save__mdb_entity_seq_cd.ref_id _item_description.description ; Identification code of the gene encoding the amino acid sequence of an entity. ; _item.name '_mdb_entity_seq_cd.ref_id' _item.category_id mdb_entity_seq_cd _item.mandatory_code no _item_type.code ucode save_ save__mdb_entity_seq_cd.ref_ac _item_description.description ; Accession number of the gene encoding the amino acid sequence of an entity. ; _item.name '_mdb_entity_seq_cd.ref_ac' _item.category_id mdb_entity_seq_cd _item.mandatory_code no _item_type.code ucode save_ save__mdb_entity_seq_cd.ref_de _item_description.description ; Short description of the gene encoding the amino acid sequence of an entity. ; _item.name '_mdb_entity_seq_cd.ref_de' _item.category_id mdb_entity_seq_cd _item.mandatory_code no _item_type.code uline save_ save__mdb_entity_seq_cd.ref_creation_date _item_description.description ; This data item holds the creation date of reference file. ; _item.name '_mdb_entity_seq_cd.ref_creation_date' _item.category_id mdb_entity_seq_cd _item.mandatory_code no _item_type.code yyyy-mm-dd save_ save__mdb_entity_seq_cd.ref_db _item_description.description ; Database containing the gene encoding the amino acid sequence of an entity. ; _item.name '_mdb_entity_seq_cd.ref_db' _item.category_id mdb_entity_seq_cd _item.mandatory_code yes _item_type.code ucode loop_ _item_examples.case _item_examples.detail Genbank ; Genbank ; NDB ; Nucleic Acid Database ; save_ save__mdb_entity_seq_cd.ref_URL _item_description.description ; URL of the database containing the gene encoding the amino acid sequence of an entity. ; _item.name '_mdb_entity_seq_cd.ref_URL' _item.category_id mdb_entity_seq_cd _item.mandatory_code no _item_type.code line save_ ######################## ## MDB_ENTITY_SEQ_MON ## ######################## save__MDB_ENTITY_SEQ_MON _category.description ; Data items in the category MDB_ENTITY_SEQ_MON record details about the monomer sequence such as reference to the original name, the database containing the sequence, the identification code, the accession code and the URL. ; _category.id mdb_entity_seq_mon _category.mandatory_code no loop_ _category_key.name '_mdb_entity_seq_mon.ref_id' '_mdb_entity_seq_mon.ref_db' loop_ _category_group.id 'inclusive_group' 'mdb_group' 'entity_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; loop_ ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__mdb_entity_seq_mon.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_mdb_entity_seq_mon.entity_id' _item.category_id mdb_entity_seq_mon _item.mandatory_code yes _item_type.code code save_ save__mdb_entity_seq_mon.ref_id _item_description.description ; Identification code of the polymeric entity. ; _item.name '_mdb_entity_seq_mon.ref_id' _item.category_id mdb_entity_seq_mon _item.mandatory_code no _item_type.code ucode save_ save__mdb_entity_seq_mon.ref_ac _item_description.description ; Accession number of the polymeric entity. ; _item.name '_mdb_entity_seq_mon.ref_ac' _item.category_id mdb_entity_seq_mon _item.mandatory_code no _item_type.code ucode save_ save__mdb_entity_seq_mon.ref_de _item_description.description ; Short description of the polymeric entity. ; _item.name '_mdb_entity_seq_mon.ref_de' _item.category_id mdb_entity_seq_mon _item.mandatory_code no _item_type.code uline save_ save__mdb_entity_seq_mon.ref_creation_date _item_description.description ; This data item refers to the creation date of reference file. ; _item.name '_mdb_entity_seq_mon.ref_creation_date' _item.category_id mdb_entity_seq_mon _item.mandatory_code no _item_type.code yyyy-mm-dd save_ save__mdb_entity_seq_mon.ref_db _item_description.description ; Database containing the polymeric entity. ; _item.name '_mdb_entity_seq_mon.ref_db' _item.category_id mdb_entity_seq_mon _item.mandatory_code yes _item_type.code ucode loop_ _item_examples.case _item_examples.detail SWP ; Swiss Prot ; NDB ; Nucleic Acid Database ; PDB ; Protein Data Bank ; save_ save__mdb_entity_seq_mon.ref_URL _item_description.description ; URL of the database containing the polymeric entity. ; _item.name '_mdb_entity_seq_mon.ref_URL' _item.category_id mdb_entity_seq_mon _item.mandatory_code no _item_type.code line save_ ########################### ## MDB_ENTITY_SEQ_RELATE ## ########################### save_MDB_ENTITY_SEQ_RELATE _category.description ; Data items in the MDB_ENTITY_SEQ_RELATE category record references to closely related polymeric entities and/or to the wild polymeric entity in case of a mutated sequence. ; _category.id mdb_entity_seq_relate _category.mandatory_code no loop_ _category_key.name '_mdb_entity_seq_relate.ref_id' '_mdb_entity_seq_relate.ref_db' loop_ _category_group.id 'inclusive_group' 'mdb_group' 'entity_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; loop_ ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__mdb_entity_seq_relate.data_src _item_description.description ; Flag to indicate if the codon sequence was submitted by the author(s) or genereted by MDB. ; _item.name '_mdb_entity_seq_relate.data_scr' _item.category_id mdb_entity_seq_relate _item.mandatory_code yes _item_type.code code _item_default.value SD loop_ _item_enumeration.value _item_enumeration.detail SD 'submitted data' GD 'generated data' save_ save__mdb_entity_seq_relate.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_mdb_entity_seq_relate.entity_id' _item.category_id mdb_entity_seq_relate _item.mandatory_code yes _item_type.code code save_ save__mdb_entity_seq_relate.ref_id _item_description.description ; Identification code of a sequence/entity closely related to the main entity(ies) described in entity_id. ; _item.name '_mdb_entity_seq_relate.ref_id' _item.category_id mdb_entity_seq_relate _item.mandatory_code no _item_type.code ucode save_ save__mdb_entity_seq_relate.ref_ac _item_description.description ; Accession number of a sequence/entity closely related to the main entity(ies) described in entity_id. ; _item.name '_mdb_entity_seq_relate.ref_ac' _item.category_id mdb_entity_seq_relate _item.mandatory_code no _item_type.code ucode save_ save__mdb_entity_seq_relate.ref_de _item_description.description ; Short description of a sequence/entity closely related to the main entity(ies) described in entity_id. ; _item.name '_mdb_entity_seq_relate.ref_de' _item.category_id mdb_entity_seq_relate _item.mandatory_code no _item_type.code uline save_ save__mdb_entity_seq_relate.ref_creation_date _item_description.description ; Entry creation date of a sequence/entity closely related to the main entity(ies) described in entity_id. ; _item.name '_mdb_entity_seq_relate.ref_creation_date' _item.category_id mdb_entity_seq_relate _item.mandatory_code no _item_type.code yyyy-mm-dd save_ save__mdb_entity_seq_relate.ref_db _item_description.description ; Database containing the sequence/entity closely related to the main entity(ies) described in entity_id. ; _item.name '_mdb_entity_seq_relate.ref_db' _item.category_id mdb_entity_seq_relate _item.mandatory_code yes _item_type.code ucode loop_ _item_examples.case _item_examples.detail SWP ; Swiss Prot ; NDB ; Nucleic Acid Database ; PDB ; Protein Data Bank ; save_ save__mdb_entity_seq_relate.ref_URL _item_description.description ; URL of the database containing the entity closely related to the entity described in _mdb_entity_seq_relate.entity_id. ; _item.name '_mdb_entity_seq_relate.ref_URL' _item.category_id mdb_entity_seq_relate _item.mandatory_code no _item_type.code line save_ save__mdb_entity_seq_relate.comparison _item_description.description ; Short description of the differences between related entities. ; _item.name '_mdb_entity_seq_relate.comparison' _item.category_id mdb_entity_seq_relate _item.mandatory_code no _item_type.code text save_ ########################## ## MDB_ENTITY_SEQ_MOTIF ## ########################## save_MDB_ENTITY_SEQ_MOTIF _category.description ; Data items in the category MDB_ENTITY_SEQ_MOTIF record details about the motif(s) and motif identification method(s). ; _category.id mdb_entity_seq_motif _category.mandatory_code no _category_key.name '_mdb_entity_seq_motif.id' loop_ _category_group.id 'inclusive_group' 'mdb_group' 'entity_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; loop_ ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__mdb_entity_seq_motif.id _item_description.description ; The value of _mdb_entity_seq_motif.id must uniquely identify a record in the MDB_ENTITY_SEQ_MOTIF list. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_mdb_entity_seq_motif.id' _item.category_id mdb_entity_seq_motif _item.mandatory_code yes _item_type.code code save_ save__mdb_entity_seq_motif.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_mdb_entity_seq_motif.entity_id' _item.category_id mdb_entity_seq_motif _item.mandatory_code yes _item_type.code code save_ save__mdb_entity_seq_motif.method _item_description.description ; Method used to identify a motif. ; _item.name '_mdb_entity_seq_motif.method' _item.category_id mdb_entity_seq_motif _item.mandatory_code no _item_type.code line save_ save__mdb_entity_seq_motif.library _item_description.description ; Library of motifs or patterns on which the search was done. ; _item.name '_mdb_entity_seq_motif.library' _item.category_id mdb_entity_seq_motif _item.mandatory_code no _item_type.code ucode save_ save__mdb_entity_seq_motif.seq _item_description.description ; Monomer sequence of the motif. ; _item.name '_mdb_entity_seq_motif.motif_seq' _item.category_id mdb_entity_seq_motif _item.mandatory_code yes _item_type.code line save_ save__mdb_entity_seq_motif.beg_mon_num _item_description.description ; This data item defines the residue number with which the motif begins in the entity, according to the full sequence of _entity_poly_seq.num. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; _item.name '_mdb_entity_seq_motif.beg_mon_num' _item.category_id mdb_entity_seq_motif _item.mandatory_code yes save_ save__mdb_entity_seq_motif.end_mon_num _item_description.description ; This data item defines the residue number with which the motif ends in the entity, according to the full sequence of _entity_poly_seq.num. This data item is a pointer to _sequence.mon_num in the ENTITY_POLY_SEQ category. ; _item.name '_mdb_entity_seq_motif.end_mon_num' _item.category_id mdb_entity_seq_motif _item.mandatory_code yes save_ save__mdb_entity_seq_motif.detail _item_description.description ; Short description of the motif. ; _item.name '_mdb_entity_seq_motif.detail' _item.category_id mdb_entity_seq_motif _item.mandatory_code no _item_type.code text save_ ############### ## MDB_MODEL ## ############### save_MDB_MODEL _category.description ; Data items in the MDB_MODEL category give details (such as the first and the end residue, etc.) about each model. ; _category.id mdb_model _category.mandatory_code yes _category_key.name '_mdb_model.id' loop_ _category_group.id 'inclusive_group' 'mdb_group' 'mdb_model_group' loop_ _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; example will be inserted later! ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__mdb_model.id _item_description.description ; The value of _mdb_model.id must uniquely identify a record in the MDB_MODEL list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_mdb_model.id' mdb_model yes '_mdb_align_search_param.mod_id' mdb_align_search_param yes '_mdb_align_thread_param.mod_id' mdb_align_thread_param yes '_mdb_align_templates.mod_id' mdb_align_templates yes '_mdb_multalign.mod_id' mdb_multalign yes '_mdb_multalign_align.mod_id' mdb_multalign_align no '_mdb_multalign_matrix.mod_id' mdb_multalign_matrix yes '_mdb_model_proc_seg.mod_id' mdb_model_proc_seg yes '_mdb_energy_min.mod_id' mdb_energy_min yes '_mdb_dynamics.mod_id' mdb_dynamics yes '_mdb_model_struct.mod_id' mdb_model_struct yes '_mdb_model_struct_src.mod_id' mdb_model_struct_src yes '_mdb_model_struct_ss.mod_id' mdb_model_struct_ss yes '_mdb_model_struct_asa.mod_id' mdb_model_struct_asa yes '_mdb_model_struct_fold.mod_id' mdb_model_struct_fold yes '_mdb_model_eval.mod_id' mdb_model_eval yes '_mdb_solved_structure.mod_id' mdb_solved_structure yes _item_type.code code loop_ _item_linked.child_name _item_linked.parent_name '_mdb_align_search_param.mod_id' '_mdb_model.id' '_mdb_align_thread_param.mod_id' '_mdb_model.id' '_mdb_align_templates.mod_id' '_mdb_model.id' '_mdb_multalign.mod_id' '_mdb_model.id' '_mdb_multalign_align.mod_id' '_mdb_model.id' '_mdb_multalign_matrix.mod_id' '_mdb_model.id' '_mdb_model_proc_seg.mod_id' '_mdb_model.id' '_mdb_energy_min.mod_id' '_mdb_model.id' '_mdb_dynamics.mod_id' '_mdb_model.id' '_mdb_model_struct.mod_id' '_mdb_model.id' '_mdb_model_struct_src.mod_id' '_mdb_model.id' '_mdb_model_struct_ss.mod_id' '_mdb_model.id' '_mdb_model_struct_asa.mod_id' '_mdb_model.id' '_mdb_model_struct_fold.mod_id' '_mdb_model.id' '_mdb_model_eval.mod_id' '_mdb_model.id' '_mdb_solved_structure.mod_id' '_mdb_model.id' save_ save__mdb_model.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_mdb_model.entity_id' _item.mandatory_code yes _item_type.code code save_ save__mdb_model.beg_mon_num _item_description.description ; This data item defines a residue number with which the model begins, according to the full sequence numbering as in _entity_poly_seq.num. This data item is a pointer to _sequence.mon_num in the ENTITY_POLY_SEQ category. ; _item.name '_mdb_model.beg_mon_num' _item.category_id mdb_model _item.mandatory_code yes _item_type.code int save_ save__mdb_model.end_mon_num _item_description.description ; This data item defines the residue number with which model ends, according to the full sequence numbering (according to _entity_poly_seq.num). This data item is a pointer to _sequence.mon_num in the ENTITY_POLY_SEQ category. ; _item.name '_mdb_model.end_mon_num' _item.category_id mdb_model _item.mandatory_code yes _item_type.code int save_ save__mdb_model.method _item_description.description ; A method used to produce the model. ; _item.name '_mdb_model.method' _item.category_id mdb_model _item.mandatory_code yes _item_type.code uline loop_ _item_enumeration.value _item_enumeration.detail 'comparative modelling' ; model generated by homology from the experimentaly determined structure of one or more homologues ; 'threading' ; fold prediction generated according to the sequence / fold search by threading ; 'de novo folding' ; model generated in absence of any parent structure for prediction ; save_ save__mdb_model.method_details _item_description.description ; This item holds description of a method or software used in modelling. ; _item.name '_mdb_model.method_details' _item.category_id mdb_model _item.mandatory_code no _item_type.code text save_ ########################### ## MDB_LIST_ALIGN_METHOD ## ########################### save_MDB_LIST_ALIGN_METHOD _category.description ; In the MDB_LIST_ALIGN_METHOD category contains a list of all the methods used to find templates. ; _category.id mdb_list_align_method _category.mandatory_code no _category_key.name '_mdb_list_align_method.id' loop_ _category_group.id 'inclusive_group' 'mdb_group' 'mdb_align_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; loop_ ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ # modification 21.02.00 _category.id # from MDB_ALIGN_METHOD_LIST to MDB_LIST_ALIGN_METHOD save__mdb_list_align_method.id _item_description.description ; The value of _mdb_align_method.id must uniquely identify a method used to find templates. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_mdb_list_align_method.id' mdb_list_align_method yes '_mdb_align_search_param.method_id' mdb_align_search_param yes '_mdb_align_thread_param.method_id' mdb_align_thread_param yes '_mdb_align_templates.method_id' mdb_align_templates yes _item_type.code code loop_ _item_linked.child_name _item_linked.parent_name '_mdb_align_search_param.method_id' '_mdb_list_align_method.id' '_mdb_align_thread_param.method_id' '_mdb_list_align_method.id' '_mdb_align_templates.method_id' '_mdb_list_align_method.id' save_ save__mdb_list_align_method.alg _item_description.description ; Procedure used to find templates. ; loop_ _item.name _item.category_id _item.mandatory_code '_mdb_list_align_method.alg' mdb_list_align_method yes _item_type.code ucode _item_examples.case FASTA save_ save__mdb_list_align_method.alg_ref _item_description.description ; Reference or additional information for the threading algorithm. ; _item.name '_mdb_list_align_method.alg_ref' _item.category_id mdb_list_align_method _item.mandatory_code no _item_type.code uline save_ save__mdb_list_align_method.details _item_description.description ; Supplementary information on procedures used to find templates. ; _item.name '_mdb_list_align_method.details' _item.category_id mdb_list_align_method _item.mandatory_code no _item_type.code text save_ ############################ ## MDB_ALIGN_SEARCH_PARAM ## ############################ save_MDB_ALIGN_SEARCH_PARAM _category.description ; Data items in the MDB_ALIGN_SEARCH_PARAM category give details of template search. ; _category.id mdb_align_search_param _category.mandatory_code no loop_ _category_key.name '_mdb_align_search_param.mod_id' '_mdb_align_search_param.method_id' loop_ _category_group.id 'inclusive_group' 'mdb_group' 'mdb_align_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; loop_ ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__mdb_align_search_param.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_mdb_align_search_param.entity_id' _item.category_id mdb_align_search_param _item.mandatory_code yes _item_type.code code save_ save__mdb_align_search_param.mod_id _item_description.description ; This data item is a pointer to _mdb_model.id in the MDB_MODEL category. ; _item.name '_mdb_align_search_param.mod_id' _item.category_id mdb_align_search_param _item.mandatory_code yes _item_type.code code save_ save__mdb_align_search_param.method_id _item_description.description ; This data item is a pointer to _mdb_list_align_method.id in the MDB_LIST_ALIGN_METHOD category. ; _item.name '_mdb_align_search_param.method_id' _item.category_id mdb_align_search_param _item.mandatory_code yes _item_type.code code save_ save__mdb_align_search_param.score_ref _item_description.description ; Short description of the alignment scoring techinque used to compare sequences. ; _item.name '_mdb_align_search_param.score_ref' _item.category_id mdb_align_search_param _item.mandatory_code yes _item_type.code uline _item_examples.case 'blastp high score' save_ save__mdb_align_search_param.subst_mtx _item_description.description ; Substitution matrix used for sequence comparison. ; _item.name '_mdb_align_search_param.subst_mtx' _item.category_id mdb_align_search_param _item.mandatory_code yes _item_type.code ucode _item_examples.case BLOSUM62 save_ save__mdb_align_search_param.filter_flag _item_description.description ; A flag to indicate whether a filter was used during database searches. ; _item.name '_mdb_align_search_param.filter_flag' _item.category_id mdb_align_search_param _item.mandatory_code yes _item_type.code ucode _item_default.value no loop_ _item_enumeration.value _item_enumeration.detail no 'no filter was used' n 'abbreviation for "no"' yes 'filter was used' y 'abbreviation for "yes"' save_ save__mdb_align_search_param.filter_ref _item_description.description ; Reference to the filter used during database searches. ; _item.name '_mdb_align_search_param.filter_ref' _item.category_id mdb_align_search_param _item.mandatory_code no _item_type.code ucode _item_examples.case DUST _item_examples.detail 'blast default filter' save_ save__mdb_align_search_param.suppl_data _item_description.description ; Supplementary information about parameters used during template searches. ; _item.name '_mdb_align_search_param.suppl_data' _item.category_id mdb_align_search_param _item.mandatory_code no _item_type.code text save_ ############################ ## MDB_ALIGN_THREAD_PARAM ## ############################ save_MDB_ALIGN_THREAD_PARAM _category.description ; Data items in the MDB_ALIGN_THREAD_PARAM category give details of template search. ; _category.id mdb_align_thread_param _category.mandatory_code no loop_ _category_key.name '_mdb_align_thread_param.mod_id' '_mdb_align_thread_param.method_id' loop_ _category_group.id 'inclusive_group' 'mdb_group' 'mdb_align_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; loop_ ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__mdb_align_thread_param.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_mdb_align_thread_param.entity_id' _item.category_id mdb_align_thread_param _item.mandatory_code yes _item_type.code code save_ save__mdb_align_thread_param.mod_id _item_description.description ; This data item is a pointer to _mdb_model.id in the MDB_MODEL category. ; _item.name '_mdb_align_thread_param.mod_id' _item.category_id mdb_align_thread_param _item.mandatory_code yes _item_type.code code save_ save__mdb_align_thread_param.method_id _item_description.description ; This data item is a pointer to _mdb_list_align_method.id in the MDB_LIST_ALIGN_METHOD category. ; _item.name '_mdb_align_thread_param.method_id' _item.category_id mdb_align_thread_param _item.mandatory_code yes _item_type.code code save_ save__mdb_align_thread_param.fold_lib _item_description.description ; Fold library. ; _item.name '_mdb_align_thread_param.fold_lib' _item.category_id mdb_align_thread_param _item.mandatory_code no _item_type.code ucode save_ save__mdb_align_thread_param.align_type _item_description.description ; Type of alignement: global or local used to compare different sequences. ; _item.name '_mdb_align_thread_param.align_type' _item.category_id mdb_align_thread_param _item.mandatory_code no _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail global 'global alignment algorithm was applied' local 'local alignment algorithm was applied' save_ save__mdb_align_thread_param.score_ref _item_description.description ; Alignment score technique. ; _item.name '_mdb_align_thread_param.score_ref' _item.category_id mdb_align_thread_param _item.mandatory_code yes _item_type.code uline _item_examples.case 'blastp high score' save_ save__mdb_align_thread_param.seq_weight _item_description.description ; Sequence weight term in the fold match. ; _item.name '_mdb_align_thread_param.seq_weight' _item.category_id mdb_align_thread_param _item.mandatory_code no _item_type.code float save_ save__mdb_align_thread_param.ss_weight _item_description.description ; Scondary structure weight term in the fold match. ; _item.name '_mdb_align_thread_param.ss_weight' _item.category_id mdb_align_thread_param _item.mandatory_code no _item_type.code float save_ save__mdb_align_thread_param.param _item_description.description ; Any additional parameter used in the evaluation of the fold (e.g. contact potential). ; _item.name '_mdb_align_thread_param.param' _item.category_id mdb_align_thread_param _item.mandatory_code no _item_type.code uline save_ save__mdb_align_thread_param.param_weight _item_description.description ; Weight term in the fold match for the paramater in _mdb_align_thread_param.param. ; _item.name '_mdb_align_thread_param.param_weight' _item.category_id mdb_align_thread_param _item.mandatory_code no _item_type.code float save_ save__mdb_align_thread_param.gap _item_description.description ; Gap introduction penality. ; _item.name '_mdb_align_thread_param.gap' _item.category_id mdb_align_thread_param _item.mandatory_code no _item_type.code float save_ save__mdb_align_thread_param.gapext _item_description.description ; Gap extention penality. ; _item.name '_mdb_align_thread_param.penalty_gapext' _item.category_id mdb_align_thread_param _item.mandatory_code no _item_type.code float save_ save__mdb_align_thread_param.suppl_data _item_description.description ; Supplementary information about parameters used during template searches. ; _item.name '_mdb_align_thread_param.suppl_data' _item.category_id mdb_align_thread_param _item.mandatory_code no _item_type.code text save_ ####################### ## MDB_LIST_TEMPLATE ## ####################### save_MDB_LIST_TEMPLATE _category.description ; Data items in MDB_LIST_TEMPLATE category store a complete list of all templates identified for all models. Some templates can be not applied for modelling. ; _category.id mdb_list_template _category.mandatory_code no _category_key.name '_mdb_list_template.id' loop_ _category_group.id 'inclusive_group' 'mdb_group' 'mdb_align_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; loop_ ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ # modification 21.02.00 _category.id # from MDB_TEMPLATE_LIST to MDB_LIST_TEMPLATE save__mdb_list_template.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_mdb_list_template.entity_id' _item.mandatory_code yes _item_type.code code save_ save__mdb_list_template.mod_id _item_description.description ; This data item is a pointer to _mdb_model.id in the MDB_MODEL category. ; _item.name '_mdb_list_template.mod_id' _item.mandatory_code yes _item_type.code code save_ save__mdb_list_template.id _item_description.description ; The value of _mdb_list_template.id must uniquely identify a template. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_mdb_list_template.id' mdb_list_template yes '_mdb_align_templates.template_id' mdb_align_templates yes '_mdb_multalign_align.template_id' mdb_multalign_align no '_mdb_multalign_matrix.template_id' mdb_multalign_matrix yes _item_type.code code loop_ _item_linked.child_name _item_linked.parent_name '_mdb_align_templates.template_id' '_mdb_list_template.id' '_mdb_multalign_align.template_id' '_mdb_list_template.id' '_mdb_multalign_matrix.template_id' '_mdb_list_template.id' save_ # '_mdb_template_atom_site.label_templ_id' mdb_template_atom_site yes # '_mdb_template_atom_site.template_id' '_mdb_list_template.id' save__mdb_list_template.ref_id _item_description.description ; Identification code of the template in the reference database. ; _item.name '_mdb_list_template.ref_id' _item.category_id mdb_list_template _item.mandatory_code no _item_type.code ucode loop_ _item_examples.case 1ABC 1PHK save_ save__mdb_list_template.ref_swp_ac _item_description.description ; Accession code of the template in the Swiss-Prot database. ; _item.name '_mdb_list_template.ref_swp_ac' _item.category_id mdb_list_template _item.mandatory_code no _item_type.code ucode loop_ _item_examples.case Q02145 POO212 save_ save__mdb_list_template.ref_de _item_description.description ; Short description of the template in the reference database. ; _item.name '_mdb_list_template.ref_de' _item.category_id mdb_list_template _item.mandatory_code no _item_type.code uline save_ save__mdb_list_template.ref_creation_date _item_description.description ; Creation date date of the template entry in the reference database. ; _item.name '_mdb_list_template.ref_creation_date' _item.category_id mdb_list_template _item.mandatory_code no _item_type.code yyyy-mm-dd loop_ _item_examples.case 1998-12-24 1996-01-06 save_ save__mdb_list_template.ref_db _item_description.description ; Name of the database containing the template entry. ; _item.name '_mdb_list_template.ref_db' _item.category_id mdb_list_template _item.mandatory_code yes _item_type.code code loop_ _item_examples.case 'PDB' 'CSD' 'Genbank' save_ ######################### ## MDB_ALIGN_TEMPLATES ## ######################### save_MDB_ALIGN_TEMPLATES _category.description ; Data items in MDB_ALIGN_TEMPLATES category store information about all templates identified for all models using different methods. ; _category.id mdb_align_templates _category.mandatory_code no loop_ _category_key.name '_mdb_align_templates.template_id' '_mdb_align_templates.method_id' '_mdb_align_templates.mod_id' loop_ _category_group.id 'inclusive_group' 'mdb_group' 'mdb_align_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; loop_ ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__mdb_align_templates.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_mdb_align_templates.entity_id' _item.category_id mdb_align_templates _item.mandatory_code yes _item_type.code code save_ save__mdb_align_templates.mod_id _item_description.description ; This data item is a pointer to _mdb_model.id in the MDB_MODEL category. ; _item.name '_mdb_align_templates.mod_id' _item.category_id mdb_align_templates _item.mandatory_code yes _item_type.code code save_ save__mdb_align_templates.template_id _item_description.description ; This data item is a pointer to _mdb_list_template.id in the MDB_LIST_TEMPLATE category. ; _item.name '_mdb_align_templates.template_id' _item.category_id mdb_align_templates _item.mandatory_code yes _item_type.code code save_ save__mdb_align_templates.method_id _item_description.description ; This data item is a pointer to _mdb_list_align_method.id in the MDB_LIST_ALIGN_METHOD category. ; _item.name '_mdb_align_templates.method_id' _item.category_id mdb_align_templates _item.mandatory_code yes _item_type.code code save_ save__mdb_align_templates.apply _item_description.description ; 'yes' indicates that this template was used in the modelling procedure, 'no' that it was not utilized to build the model. ; _item.name '_mdb_align_templates.apply' _item.category_id mdb_align_templates _item.mandatory_code yes _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail no 'not applied' n 'abbreviation for "no"' yes 'applied in the modelling procedure' y 'abbreviation for "yes"' save_ save__mdb_align_templates.score _item_description.description ; Score value for the alignement template-target in accordance to _mdb_align_search_param.score_ref or _mdb_align_thread_param.score_ref data items. ; loop_ _item.name _item.category_id _item.mandatory_code '_mdb_align_templates.score' mdb_align_templates yes _item_type.code float loop_ _item_linked.child_name _item_linked.parent_name '_mdb_align_templates.score' '_mdb_align_templates.score' save_ save__mdb_align_templates.probability _item_description.description ; Probability value for the alignment template-target. ; _item.name '_mdb_align_templates.probability' _item.category_id mdb_align_templates _item.mandatory_code no _item_type.code float save_ save__mdb_align_templates.pc_identity _item_description.description ; Percentage of identity between the template (_mdb_align_templates.id) and the target (_mdb_align_templates.mod_id) sequences. ; _item.name '_mdb_align_templates.pc_identity' _item.category_id mdb_align_templates _item.mandatory_code no _item_type.code float save_ save__mdb_align_templates.refine_ls_d_res_high _item_description.description ; The highest resolution in angstroms for the interplanar spacing in the reflection data used in refinement. This is the smallest d value. ; _item.name '_mdb_align_templates.refine_ls_d_res_high' _item.category_id mdb_align_templates _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__mdb_align_templates.refine_ls_d_res_low _item_description.description ; The lowest resolution in ansgtroms for the interplanar spacing in the reflection data used in refinement. This is the largest d value. ; _item.name '_mdb_align_templates.refine_ls_d_res_low' _item.category_id mdb_align_templates _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__mdb_align_templates.refine_ls_R_factor_all _item_description.description ; Residual factor R for all reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure factor amplitudes F~calc~ = the calculated structure factor amplitudes sum is taken over the specified reflections ; _item.name '_mdb_align_templates.refine_ls_R_factor_all' _item.category_id mdb_align_templates _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__mdb_align_templates.refine_ls_R_factor_R_free _item_description.description ; Residual factor R for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test (i.e., excluded from refinement) reflections when refinement included calculation of a "free" R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure factor amplitudes F~calc~ = the calculated structure factor amplitudes sum is taken over the specified reflections ; _item.name '_mdb_align_templates.refine_ls_R_factor_R_free' _item.category_id mdb_align_templates _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__mdb_align_templates.refine_ls_R_factor_R_work _item_description.description ; Residual factor R for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working (i.e., included in refinement) reflections when refinement included calculation of a "free" R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. _refine.ls_R_factor_obs should not be confused with _refine.ls_R_factor_R_work; the former reports the results of a refinement in which all observed reflections were used, the latter a refinement in which a subset of the observed reflections were excluded from refinement for the calculation of a "free" R factor. However, it would be meaningful to quote both values if a "free" R factor were calculated for most of the refinement, but all of the observed reflections were used in the final rounds of refinement; such a protocol should be explained in _refine.details. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure factor amplitudes F~calc~ = the calculated structure factor amplitudes sum is taken over the specified reflections ; _item.name '_mdb_align_templates.refine_ls_R_factor_R_work' _item.category_id mdb_align_templates _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ ################### ## MDB_MULTALIGN ## ################### save_MDB_MULTALIGN _category.description ; Data items in this category store information on multiple alignments of templates and targets. ; _category.id mdb_multalign _category.mandatory_code yes _category_key.name '_mdb_multalign.align_num' loop_ _category_group.id 'inclusive_group' 'mdb_group' 'mdb_align_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; loop_ ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__mdb_multalign.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_mdb_multalign.entity_id' _item.category_id mdb_multalign _item.mandatory_code no _item_type.code code save_ save__mdb_multalign.mod_id _item_description.description ; This data item is a pointer to _mdb_model.id in the MDB_MODEL category. ; _item.name '_mdb_multalign.mod_id' _item.category_id mdb_multalign _item.mandatory_code yes _item_type.code code save_ save__mdb_multalign.align_num _item_description.description ; The value of _mdb_multalign.align_num must uniquely identify a record in the MDB_MULTALIGN category. It is the number identifying each alignement. Note that this item needs to be a number. ; loop_ _item.name _item.category_id _item.mandatory_code '_mdb_multalign.align_num' mdb_multalign yes '_mdb_multalign_align.num' mdb_multalign_align yes loop_ _item_linked.child_name _item_linked.parent_name '_mdb_multalign_align.num' '_mdb_multalign.align_num' loop_ _item_range.maximum _item_range.minimum . 1 1 1 _item_type.code int save_ save__mdb_multalign.nseq _item_description.description ; Total number of aligned sequences (target and templates) for each model. ; _item.name '_mdb_multalign.nseq' _item.category_id mdb_multalign _item.mandatory_code yes _item_type.code int loop_ _item_range.maximum _item_range.minimum . 1 1 1 save_ save__mdb_multalign.length _item_description.description ; Number of positions in the alignment (length) including gaps for each model. ; _item.name '_mdb_multalign.length' _item.category_id mdb_multalign _item.mandatory_code yes _item_type.code int loop_ _item_range.maximum _item_range.minimum . 1 1 1 save_ save__mdb_multalign.view _item_description.description ; Visual representation of the multiple alignment including gaps for each model. ; _item.name '_mdb_multalign.view' _item.category_id mdb_multalign _item.mandatory_code no _item_type.code text save_ ######################### ## MDB_MULTALIGN_ALIGN ## ######################### save__MDB_MULTALIGN_ALIGN _category.description ; Data items in the MDB_MULTALIGN_ALIGN category contain the aligned sequences. ; _category.id mdb_multalign_align _category.mandatory_code no loop_ _category_key.name '_mdb_multalign_align.num' '_mdb_multalign_align.seq_pos' '_mdb_multalign_align.mon_pos' loop_ _category_group.id 'inclusive_group' 'mdb_group' 'mdb_align_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; loop_ ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__mdb_multalign_align.mod_id _item_description.description ; This data item is a pointer to _mdb_model.id in the MDB_MODEL category. ; _item.name '_mdb_multalign_align.mod_id' _item.category_id mdb_multalign_align _item.mandatory_code no _item_type.code code save_ save__mdb_multalign_align.template_id _item_description.description ; This data item is a pointer to _mdb_list_template.id in the MDB_LIST_TEMPLATE category. ; _item.name '_mdb_multalign_align.template_id' _item.category_id mdb_multalign_align _item.mandatory_code no _item_type.code code save_ save__mdb_multalign_align.mon_id _item_description.description ; Monomer sequence for target and template(s) including gaps which are identified as '-'. ; _item.name '_mdb_multalign_align.mon_id' _item.category_id mdb_multalign_align _item.mandatory_code yes _item_type.code code save_ save__mdb_multalign_align.num _item_description.description ; This data item is a pointer to _mdb_multalign.align_num in the MDB_MULTALIGN category. ; _item.name '_mdb_multalign_align.num' _item.category_id mdb_multalign_align _item.mandatory_code yes _item_type.code int save_ save__mdb_multalign_align.seq_pos _item_description.description ; This data item must uniquely and sequentially (target, first template, second template, ect.) identify the target and template sequences for each alignment. ; _item.name '_mdb_multalign_align.seq_pos' _item.category_id mdb_multalign_align _item.mandatory_code yes _item_type.code int loop_ _item_range.maximum _item_range.minimum . 1 1 1 save_ save__mdb_multalign_align.mon_pos _item_description.description ; This data item must uniquely and sequentially identify the monomer and gap positions for each alignment. ; _item.name '_mdb_multalign_align.mon_pos' _item.category_id mdb_multalign_align _item.mandatory_code yes _item_type.code int loop_ _item_range.maximum _item_range.minimum . 1 1 1 save_ ########################## ## MDB_MULTALIGN_MATRIX ## ########################## save_MDB_MULTALIGN_MATRIX _category.description ; The MDB_MULTALIGN_MATRIX category provides placeholders for transformation matrices and vectors of each template, describing transformations from initial coordinates to final coordinates in the multiple alignment superposition. ; _category.id mdb_multalign_matrix _category.mandatory_code no loop_ _category_key.name '_mdb_multalign_matrix.mod_id' '_mdb_multalign_matrix.template_id' loop_ _category_group.id 'inclusive_group' 'mdb_group' 'mdb_align_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; loop_ ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__mdb_multalign_matrix.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_mdb_multalign_matrix.entity_id' _item.category_id mdb_multalign_matrix _item.mandatory_code yes _item_type.code code save_ save__mdb_multalign_matrix.mod_id _item_description.description ; This data item is a pointer to _mdb_model.id in the MDB_MODEL category. ; _item.name '_mdb_multalign_matrix.mod_id' _item.category_id mdb_multalign_matrix _item.mandatory_code yes _item_type.code code save_ save__mdb_multalign_matrix.template_id _item_description.description ; This data item is a pointer to _mdb_list_template.id in the MDB_LIST_TEMPLATE category. ; _item.name '_mdb_multalign_matrix.template_id' _item.category_id mdb_multalign_matrix _item.mandatory_code yes _item_type.code code save_ save__mdb_multalign_matrix.trans[1][1] _item_description.description ; The [1][1] element of the transformation matrix. ; _item.name '_mdb_multalign_matrix.trans[1][1]' _item.category_id mdb_multalign_matrix _item.mandatory_code no _item_default.value 1.0 _item_sub_category.id matrix _item_type.code float save_ save__mdb_multalign_matrix.trans[1][2] _item_description.description ; The [1][2] element of the transformation matrix. ; _item.name '_mdb_multalign_matrix.trans[1][2]' _item.category_id mdb_multalign_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__mdb_multalign_matrix.trans[1][3] _item_description.description ; The [1][3] element of the transformation matrix. ; _item.name '_mdb_multalign_matrix.trans[1][3]' _item.category_id mdb_multalign_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__mdb_multalign_matrix.trans[2][1] _item_description.description ; The [2][1] element of the transformation matrix. ; _item.name '_mdb_multalign_matrix.trans[2][1]' _item.category_id mdb_multalign_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__mdb_multalign_matrix.trans[2][2] _item_description.description ; The [2][2] element of the transformation matrix. ; _item.name '_mdb_multalign_matrix.trans[2][2]' _item.category_id mdb_multalign_matrix _item.mandatory_code no _item_default.value 1.0 _item_sub_category.id matrix _item_type.code float save_ save__mdb_multalign_matrix.trans[2][3] _item_description.description ; The [2][3] element of the transformation matrix. ; _item.name '_mdb_multalign_matrix.trans[2][3]' _item.category_id mdb_multalign_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__mdb_multalign_matrix.trans[3][1] _item_description.description ; The [3][1] element of the transformation matrix. ; _item.name '_mdb_multalign_matrix.trans[3][1]' _item.category_id mdb_multalign_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__mdb_multalign_matrix.trans[3][2] _item_description.description ; The [3][2] element of the transformation matrix. ; _item.name '_mdb_multalign_matrix.trans[3][2]' _item.category_id mdb_multalign_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__mdb_multalign_matrix.trans[3][3] _item_description.description ; The [3][3] element of the transformation matrix. ; _item.name '_mdb_multalign_matrix.trans[3][3]' _item.category_id mdb_multalign_matrix _item.mandatory_code no _item_default.value 1.0 _item_sub_category.id matrix _item_type.code float save_ save__mdb_multalign_matrix.trans_vector[1] _item_description.description ; The [1] element of the transformation vector. ; _item.name '_mdb_multalign_matrix.trans_vector[1]' _item.category_id mdb_multalign_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__mdb_multalign_matrix.trans_vector[2] _item_description.description ; The [2] element of the transformation vector. ; _item.name '_mdb_multalign_matrix.trans_vector[2]' _item.category_id mdb_multalign_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__mdb_multalign_matrix.trans_vector[3] _item_description.description ; The [3] element of the transformation vector. ; _item.name '_mdb_multalign_matrix.trans_vector[3]' _item.category_id mdb_multalign_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ ######################## ## MDB_MODEL_PROC_SEG ## ######################## save_MDB_MODEL_PROC_SEG _category.description ; Model building procedure for segments in models; there can be more than one segment per model. ; _category.id mdb_model_proc_seg _category.mandatory_code no _category_key.name '_mdb_model_proc_seg.id' loop_ _category_group.id 'inclusive_group' 'mdb_group' 'mdb_model_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; loop_ ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__mdb_model_proc_seg.id _item_description.description ; The value of _mdb_model_proc_seg.id must uniquely identify a record in the MDB_MODEL_PROC_SEG list. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_mdb_model_proc_seg.id' _item.category_id mdb_model_proc_seg _item.mandatory_code yes _item_type.code code save_ save__mdb_model_proc_seg.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_mdb_model_proc_seg.entity_id' _item.category_id mdb_model_proc_seg _item.mandatory_code no _item_type.code code save_ save__mdb_model_proc_seg.mod_id _item_description.description ; This data item is a pointer to _mdb_model.id in the MDB_MODEL category. ; _item.name '_mdb_model_proc_seg.mod_id' _item.category_id mdb_model_proc_seg _item.mandatory_code yes _item_type.code code save_ save__mdb_model_proc_seg.method_id _item_description.description ; This data item is a pointer to _mdb_model_param.method_id in the MDB_MODEL_PARAM category. ; _item.name '_mdb_model_proc_seg.method_id' _item.category_id mdb_model_proc_seg _item.mandatory_code yes _item_type.code code save_ save__mdb_model_proc_seg.beg_mon_num _item_description.description ; This data item defines the residue number with which the segment begins, according to the full sequence numbering _entity_poly_seq.num. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; _item.name '_mdb_model_proc_seg.beg_mon_num' _item.category_id mdb_model_proc_seg _item.mandatory_code yes _item_type.code code save_ save__mdb_model_proc_seg.end_mon_num _item_description.description ; This data item defines the residue number with which the segment ends, according to the full sequence numbering _entity_poly_seq.num. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; _item.name '_mdb_model_proc_seg.end_mon_num' _item.category_id mdb_model_proc_seg _item.mandatory_code yes _item_type.code code save_ save__mdb_model_proc_seg.conservation _item_description.description ; This data item shows if the segment is defined as a structurally conserved or variable region, or undefined. ; _item.name '_mdb_model_proc_seg.conservation' _item.category_id mdb_model_proc_seg _item.mandatory_code no _item_type.code code loop_ _item_enumeration.value conserved variable undefined save_ save__mdb_model_proc_seg.type _item_description.description ; This data item shows the segment attribution i.e. backbone or side chains or both. ; _item.name '_mdb_model_proc_seg.type' _item.category_id mdb_model_proc_seg _item.mandatory_code yes _item_type.code code loop_ _item_enumeration.value backbone side_chains back_side_ch save_ save__mdb_model_proc_seg.template _item_description.description ; This data item shows the type of template used for the segment single template, multiple templates, or averaged from multiple template structure. ; _item.name '_mdb_model_proc_seg.template' _item.category_id mdb_model_proc_seg _item.mandatory_code no _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail single_template 'single template from parent structure(s)' multiple_template 'multiple templates from parent structures' avarage_template 'averaged template from parent structures' save_ save__mdb_model_proc_seg.build _item_description.description ; This data item shows if the segement is modelled from a parent structure(s), databse search, or generated de novo. ; _item.name '_mdb_model_proc_seg.build' _item.category_id mdb_model_proc_seg _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value _item_enumeration.detail parent_template 'template generated' db_search 'database search generated' de_novo 'de novo generated' save_ save__mdb_model_proc_seg.details _item_description.description ; This data item gives details of the model building. ; _item.name '_mdb_model_proc_seg.details' _item.category_id mdb_model_proc_seg _item.mandatory_code no _item_type.code text save_ ##################### ## MDB_FORCE_FIELD ## ##################### save_MDB_FORCE_FIELD _category.description ; Data items in the MDB_FORCE_FIELD category specify the force field used for energy calculations, the version and the possible modifications. ; _category.id mdb_force_field _category.mandatory_code no _category_key.name '_mdb_force_field.id' loop_ _category_group.id 'inclusive_group' 'mdb_group' 'mdb_calc_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; loop_ ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__mdb_force_field.id _item_description.description ; The value of _mdb_force_field.id must uniquely identify a record in the MDB_FORCE_FIELD list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_mdb_force_field.id' mdb_force_field yes '_mdb_energy_min.ff_id' mdb_energy_min no '_mdb_dynamics.ff_id' mdb_dynamics no _item_type.code code loop_ _item_linked.child_name _item_linked.parent_name '_mdb_energy_min.ff_id' '_mdb_force_field.id' '_mdb_dynamics.ff_id' '_mdb_force_field.id' save_ save__mdb_force_field.name _item_description.description ; Force field name. ; _item.name '_mdb_force_field.name' _item.category_id mdb_force_field _item.mandatory_code yes _item_type.code code loop_ _item_examples.case 'AMBER' 'GROMOS' 'CHARMM' save_ save__mdb_force_field.version _item_description.description ; Force field version. ; _item.name '_mdb_force_field.version' _item.category_id mdb_force_field _item.mandatory_code yes _item_type.code code loop_ _item_examples.case '1.4' '23' save_ save__mdb_force_field.modified _item_description.description ; 'yes' indicates that modifications were applied to the original force field, 'no' that no modifications were applied. ; _item.name '_mdb_force_field.modified' _item.category_id mdb_force_field _item.mandatory_code no _item_type.code ucode _item_default.value no loop_ _item_enumeration.value _item_enumeration.detail no 'no modification' n 'abbreviation for "no"' yes 'some modifications were introduced in the original force field' y 'abbreviation for "yes"' save_ save__mdb_force_field.non_std_param _item_description.description ; Short description of the modified or added parameters. ; _item.name '_mdb_force_field.non_std_param' _item.category_id mdb_force_field _item.mandatory_code no _item_type.code text save_ ################# ## MDB_SOLVENT ## ################# save_MDB_SOLVENT _category.description ; Data items in the MDB_SOLVENT category store information on the solvent. ; _category.id mdb_solvent _category.mandatory_code no _category_key.name '_mdb_solvent.id' loop_ _category_group.id 'inclusive_group' 'mdb_group' 'mdb_calc_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; loop_ ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__mdb_solvent.id _item_description.description ; The value of _mdb_model.id must uniquely identify a record in the MDB_SOLVENT list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_mdb_solvent.id' mdb_solvent yes '_mdb_energy_min.solv_id' mdb_energy_min no '_mdb_dynamics.solv_id' mdb_dynamics no _item_type.code code loop_ _item_linked.child_name _item_linked.parent_name '_mdb_energy_min.solv_id' '_mdb_solvent.id' '_mdb_dynamics.solv_id' '_mdb_solvent.id' save_ save__mdb_solvent.solv_type _item_description.description ; Type of solvent used (e.g. water). ; _item.name '_mdb_solvent.solv_type' _item.category_id mdb_solvent _item.mandatory_code no _item_type.code uline save_ save__mdb_solvent.solv_model _item_description.description ; Model used to simulate the solvent: explicit or continuum. ; _item.name '_mdb_solvent.solv_model' _item.category_id mdb_solvent _item.mandatory_code no _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail explicit ; Each molecule of solvent is explicitally taken into account. ; continuum ; No explicit solvent molecules are considered. ; save_ save__mdb_solvent.solv_model_spec _item_description.description ; Specific model used to simulate the solvent. ; _item.name '_mdb_solvent.solv_model_spec' _item.category_id mdb_solvent _item.mandatory_code no _item_type.code uline loop_ _item_examples.case 'SPC' 'TIP3P' 'TIP4P' 'ST2' save_ save__mdb_solvent.solv_model_ref _item_description.description ; Short description or publication reference for the used model. ; _item.name '_mdb_solvent.solv_ref_model' _item.category_id mdb_solvent _item.mandatory_code no _item_type.code text save_ #################### ## MDB_ENERGY_MIN ## #################### save_MDB_ENERGY_MIN _category.description ; Data items in the MDB_ENERGY_MIN category specify parameters used during the energy minimisation. ; _category.id mdb_energy_min _category.mandatory_code no _category_key.name '_mdb_energy_min.step_id' loop_ _category_group.id 'inclusive_group' 'mdb_group' 'mdb_calc_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; loop_ ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__mdb_energy_min.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_mdb_energy_min.entity_id' _item.category_id mdb_energy_min _item.mandatory_code no _item_type.code code save_ save__mdb_energy_min.mod_id _item_description.description ; This data item is a pointer to _mdb_model.id in the MDB_MODEL category. ; _item.name '_mdb_energy_min.mod_id' _item.category_id mdb_energy_min _item.mandatory_code yes _item_type.code code save_ save__mdb_energy_min.seg_id _item_description.description ; This data item is a pointer to _mdb_model_struc_seg.id in the MDB_MODEL_STRUC_SEG category. ; _item.name '_mdb_energy_min.seg_id' _item.category_id mdb_energy_min _item.mandatory_code yes _item_type.code code save_ save__mdb_energy_min.step_id _item_description.description ; The value of _mdb_energy_min.step_id must uniquely identify each minimisation step for each _mdb_energy_min.seg_id. Note that this item need not be a number it can be any unique identifier of each minimisation event. ; _item.name '_mdb_energy_min.step_id' _item.category_id mdb_energy_min _item.mandatory_code yes _item_type.code ucode save_ save__mdb_energy_min.ff_id _item_description.description ; This data item is a pointer to _mdb_force_field.id in the category MDB_FORCE_FIELD. ; _item.name '_mdb_energy_min.ff_id' _item.category_id mdb_energy_min _item.mandatory_code yes _item_type.code code save_ save__mdb_energy_min.method _item_description.description ; Minimisation technique. ; _item.name '_mdb_energy_min.method' _item.category_id mdb_energy_min _item.mandatory_code yes _item_type.code uline loop_ _item_examples.case 'steepest descent' 'conjugate gradient' 'Newton-Raphson' save_ save__mdb_energy_min.cycle_num _item_description.description ; Number of minimisation cycles allowed. ; loop_ _item.name '_mdb_energy_min.cycle_num' _item.category_id mdb_energy_min _item.mandatory_code no _item_type.code int save_ save__mdb_energy_min.grms_conv _item_description.description ; Root mean square gradient convergence criterion. ; _item.name '_mdb_energy_min.grms_conv' _item.category_id mdb_energy_min _item.mandatory_code no _item_type.code float _item_units.code kilocalories_per_mole_angstroms save_ save__mdb_energy_min.en_conv _item_description.description ; Convergence criterion based on the energy difference between successive steps. ; _item.name '_mdb_energy_min.en_conv' _item.category_id mdb_energy_min _item.mandatory_code no _item_type.code float _item_units.code kilocalories_per_moles save_ save__mdb_energy_min.coord_conv _item_description.description ; Convergence criterion based on the change in coordinates (displacement) between successive steps. ; _item.name '_mdb_energy_min.coord_conv' _item.category_id mdb_energy_min _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ save__mdb_energy_min.atom_def _item_description.description ; This data item shows if the energy minimisation is conducted using the united atom approximation or all atoms. ; _item.name '_mdb_energy_min.atom_def' _item.category_id mdb_energy_min _item.mandatory_code no _item_type.code code loop_ _item_enumeration.value all_atom united_atom save_ save__mdb_energy_min.charge _item_description.description ; Type of charges. ; _item.name '_mdb_energy_min.charge' _item.category_id mdb_energy_min _item.mandatory_code no _item_type.code line save_ save__mdb_energy_min.pH _item_description.description ; pH value used to protonate residues. ; _item.name '_mdb_energy_min.pH' _item.category_id mdb_energy_min _item.mandatory_code no _item_type.code float save_ save__mdb_energy_min.dielectr_const _item_description.description ; Dielectric constant. ; _item.name '_mdb_energy_min.dielectr_const' _item.category_id mdb_energy_min _item.mandatory_code no _item_type.code float save_ save__mdb_energy_min.dielectr_func _item_description.description ; Dielectric function. ; _item.name '_mdb_energy_min.dielectr_func' _item.category_id mdb_energy_min _item.mandatory_code no _item_type.code line save_ save__mdb_energy_min.nbi_cutoff _item_description.description ; Distance cutoff for non bonded interaction. ; _item.name '_mdb_energy_min.nbi_cutoff' _item.category_id mdb_energy_min _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ save__mdb_energy_min.constr _item_description.description ; Constraints applied during energy minimisation. ; _item.name '_mdb_energy_min.constr' _item.category_id mdb_energy_min _item.mandatory_code no _item_type.code code loop_ _item_enumeration.value fixed relaxed function save_ save__mdb_energy_min.constr_func _item_description.description ; Type of function used to define constraints applied during energy minimisation. ; _item.name '_mdb_energy_min.constr_func' _item.category_id mdb_energy_min _item.mandatory_code no _item_type.code line save_ save__mdb_energy_min.constr_suppl_data _item_description.description ; Additional information on the applied constraints. ; _item.name '_mdb_energy_min.constr_suppl_data' _item.category_id mdb_energy_min _item.mandatory_code no _item_type.code text save_ save__mdb_energy_min.solv_flag _item_description.description ; Flag indicating if a solvent model was used. ; _item.name '_mdb_energy_min.solv_flag' _item.category_id mdb_energy_min _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail yes 'solvent model used' y 'abbreviation for "yes"' no 'no solvent model used' n 'abbreviation for "no"' save_ save__mdb_energy_min.solv_id _item_description.description ; This data item is a pointer to _mdb_solvent.id in the MDB_SOLVENT category. ; _item.name '_mdb_energy_min.solv_id' _item.category_id mdb_energy_min _item.mandatory_code no save_ ################## ## MDB_DYNAMICS ## ################## save_MDB_DYNAMICS _category.description ; Data items in the MDB_DYNAMICS category store information about the application of molecular dynamics simulations for each step. ; _category.id mdb_dynamics _category.mandatory_code no _category_key.name '_mdb_dynamics.step_id' loop_ _category_group.id 'inclusive_group' 'mdb_group' 'mdb_calc_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; loop_ ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__mdb_dynamics.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_mdb_dynamics.entity_id' _item.category_id mdb_dynamics _item.mandatory_code no _item_type.code code save_ save__mdb_dynamics.mod_id _item_description.description ; This data item is a pointer to _mdb_model.id in the MDB_MODEL category. ; _item.name '_mdb_dynamics.mod_id' _item.category_id mdb_dynamics _item.mandatory_code yes _item_type.code code save_ save__mdb_dynamics.seg_id _item_description.description ; This data item is a pointer to _mdb_model_struc_seg.id in the MDB_MODEL_STRUC_SEG category. ; _item.name '_mdb_dynamics.seg_id' _item.category_id mdb_dynamics _item.mandatory_code yes _item_type.code code save_ save__mdb_dynamics.step_id _item_description.description ; The value of _mdb_dynamics.step_id must uniquely identify each step of molecular dynamics for each _mdb_dynamics.seg_id. Note that this item need not be a number it can be any unique identifier of each molecular dynamics step. ; _item.name '_mdb_dynamics.step_id' _item.category_id mdb_dynamics _item.mandatory_code yes _item_type.code ucode save_ save__mdb_dynamics.method _item_description.description ; Dynammics technique. ; _item.name '_mdb_dynamics.method' _item.category_id mdb_dynamics _item.mandatory_code yes _item_type.code uline loop_ _item_examples.case 'Langevin' 'constant temperature' 'constant pressure' save_ save__mdb_dynamics.temp_control _item_description.description ; Temperature control model. ; _item.name '_mdb_dynamics.temp_control' _item.category_id mdb_dynamics _item.mandatory_code no _item_type.code uline loop_ _item_examples.case 'velocity scaling' 'Berendsen temperature bath' 'Nose-Hoover dynamics' save_ save__mdb_dynamics.temp_start _item_description.description ; Starting temperature. ; _item.name '_mdb_dynamics.temp_start' _item.category_id mdb_dynamics _item.mandatory_code no _item_type.code float _item_units.code kelvins save_ save__mdb_dynamics.temp_stop _item_description.description ; Ending temperature. ; _item.name '_mdb_dynamics.temp_stop' _item.category_id mdb_dynamics _item.mandatory_code no _item_type.code float _item_units.code kelvins save_ save__mdb_dynamics.simulation_time _item_description.description ; Length of the simulation. ; _item.name '_mdb_dynamics.simulation_time' _item.category_id mdb_dynamics _item.mandatory_code no _item_type.code float _item_units.code picoseconds save_ save__mdb_dynamics.time_step _item_description.description ; Integration time step for the simulation (dt). ; _item.name '_mdb_dynamics.time_step' _item.category_id mdb_dynamics _item.mandatory_code no _item_type.code float _item_units.code femtoseconds save_ save__mdb_dynamics.constr _item_description.description ; Constraints applied during dynamics simulation. ; _item.name '_mdb_dynamics.constr' _item.category_id mdb_dynamics _item.mandatory_code no _item_type.code code loop_ _item_enumeration.value fixed relaxed function save_ save__mdb_dynamics.constr_func _item_description.description ; Type of function used to define constraints applied during dynamics simulation. ; _item.name '_mdb_dynamics.constr_func' _item.category_id mdb_dynamics _item.mandatory_code no _item_type.code line save_ save__mdb_dynamics.suppl_data _item_description.description ; Additional information on the applied constraints. ; _item.name '_mdb_dynamics.suppl_data' _item.category_id mdb_dynamics _item.mandatory_code no _item_type.code text save_ save__mdb_dynamics.boundary_cond_x _item_description.description ; Boundary extention from the furthermost dimension of the modelled molecule in the X direction. ; _item.name '_mdb_dynamics.boundary_cond_x' _item.category_id mdb_dynamics _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ save__mdb_dynamics.boundary_cond_y _item_description.description ; Boundary extention from the furthermost dimension of the modelled molecule in the Y direction. ; _item.name '_mdb_dynamics.boundary_cond_y' _item.category_id mdb_dynamics _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ save__mdb_dynamics.boundary_cond_z _item_description.description ; Boundary extention from the furthermost dimension of the modelled molecule in the Z direction. ; _item.name '_mdb_dynamics.boundary_cond_z' _item.category_id mdb_dynamics _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ save__mdb_dynamics.boundary_cond_details _item_description.description ; Boundary condition details. ; _item.name '_mdb_dynamics.boundary_cond_details' _item.category_id mdb_dynamics _item.mandatory_code no _item_type.code text save_ save__mdb_dynamics.ff_id _item_description.description ; This data item is a pointer to _mdb_force_field.id in the category MDB_FORCE_FIELD. ; _item.name '_mdb_dynamics.ff_id' _item.category_id mdb_dynamics _item.mandatory_code yes _item_type.code code save_ save__mdb_dynamics.charge _item_description.description ; Type of charges used. ; _item.name '_mdb_dynamics.charge' _item.category_id mdb_dynamics _item.mandatory_code no _item_type.code uline save_ save__mdb_dynamics.solv_flag _item_description.description ; Flag indicating if a solvent model was used. ; _item.name '_mdb_dynamics.solv_flag' _item.category_id mdb_dynamics _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail yes 'solvent model used' y 'abbreviation for "yes"' no 'no solvent model used' n 'abbreviation for "no"' save_ save__mdb_dynamics.solv_id _item_description.description ; This data item is a pointer to _mdb_solvent.id in the MDB_SOLVENT category. ; _item.name '_mdb_dynamics.solv_id' _item.category_id mdb_dynamics _item.mandatory_code no _item_type.code code save_ ###################### ## MDB_MODEL_STRUCT ## ###################### save_MDB_MODEL_STRUCT _category.description ; Date items in the MDB_MODEL_STRUCT category record details of definition, description and quality for each model on a residue basis level. ; _category.id mdb_model_struct _category.mandatory_code yes loop_ _category_key.name '_mdb_model_struct.mod_id' '_mdb_model_struct.entity_mon_num' loop_ _category_group.id 'inclusive_group' 'mdb_group' 'mdb_model_struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; loop_ ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__mdb_model_struct.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_mdb_model_struct.entity_id' _item.category_id mdb_model_struct _item.mandatory_code yes _item_type.code code save_ save__mdb_model_struct.mod_id _item_description.description ; This data item is a pointer to _mdb_model.id in the MDB_MODEL category. ; _item.name '_mdb_model_struct.mod_id' _item.category_id mdb_model_struct _item.mandatory_code yes _item_type.code code save_ save__mdb_model_struct.mon_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_mdb_model_struct.mon_id' _item.category_id mdb_model_struct _item.mandatory_code yes save_ save__mdb_model_struct.entity_mon_num _item_description.description ; This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; _item.name '_mdb_model_struct.entity_mon_num' _item.category_id mdb_model_struct _item.mandatory_code yes save_ save__mdb_model_struct.align_match _item_description.description ; Type of alignment match for each residue in the alignment with template(s). ; _item.name '_mdb_model_struct.align_match' _item.category_id mdb_model_struct _item.mandatory_code no _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail F 'full' P 'partial' N 'no' save_ save__mdb_model_struct.align_consens_id _item_description.description ; Consensus sequence for the alignment with template(s) (at a monomer level). ; _item.name '_mdb_model_struct.align_consens_id' _item.category_id mdb_model_struct _item.mandatory_code no _item_type.code ucode save_ save__mdb_model_struct.align_cons_probability _item_description.description ; Conservation probability in the alignment (at a monomer level). ; _item.name '_mdb_model_struct.align_cons_probability' _item.category_id mdb_model_struct _item.mandatory_code no _item_type.code float save_ save__mdb_model_struct.ss _item_description.description ; Secondary structure associated with each residue. More information on secondary structure (criteria and model) can be found in the category MDB_MODEL_STRUCT_SS. ; _item.name '_mdb_model_struct.ss' _item.category_id mdb_model_struct _item.mandatory_code no _item_type.code ucode save_ save__mdb_model_struct.asa _item_description.description ; Solvent accessibility associated with each residue. More information on solvent accessibility (used criteria and model) are found in the category MDB_MODEL_STRUCT_ASA. ; _item.name '_mdb_model_struct.asa' _item.category_id mdb_model_struct _item.mandatory_code no _item_type.code ucode save_ save__mdb_model_struct.accuracy_bond_length _item_description.description ; Estimation of the bonds accuracy on a residue level. #need to revise, dummy range values used! ; _item.name '_mdb_model_struct.accuracy_bond_length' _item.category_id mdb_model_struct _item.mandatory_code no _item_type.code int loop_ _item_range.maximum _item_range.minimum 10 10 10 1 1 1 save_ save__mdb_model_struct.accuracy_bond_angle _item_description.description ; Estimation of the bond angles accuracy on a residue level. #need to revise, dummy range values used! ; _item.name '_mdb_model_struct.accuracy_bond_angle' _item.category_id mdb_model_struct _item.mandatory_code no _item_type.code int loop_ _item_range.maximum _item_range.minimum 10 10 10 1 1 1 save_ save__mdb_model_struct.accuracy_tors_angle _item_description.description ; Estimation of the torsion angles accuracy on a residue level residue. #need to revise, dummy range values used! ; _item.name '_mdb_model_struct.accuracy_tors_angle' _item.category_id mdb_model_struct _item.mandatory_code no _item_type.code int loop_ _item_range.maximum _item_range.minimum 10 10 10 1 1 1 save_ save__mdb_model_struct.C_factor _item_description.description ; Confidence factor per residue. The Model C-factor is computed as: 50.0 * (1/ number selected templates) and 100.0 for all atoms added during loop and side-chain building. #need to revise! ; _item.name '_mdb_model_struct.C_factor' _item.category_id mdb_model_struct _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum 0.0 0.0 100.0 0.0 100.0 100.0 _item_type.code float save_ ########################## ## MDB_MODEL_STRUCT_SRC ## ########################## save_MDB_MODEL_STRUCT_SRC _category.description ; Data items in the MDB_MODEL_STRUCT_SRC category specify the source of some data items present in the MDB_MODEL_STRUCT category. These data items can be submitted by the author(s) of the model/entry or generated automatically by MDB. SD stands for submitted data and GD for generated data. ; _category.id mdb_model_struct_src _category.mandatory_code no _category_key.name '_mdb_model_struct_src.mod_id' loop_ _category_group.id 'inclusive_group' 'mdb_group' 'mdb_model_struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; loop_ ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__mdb_model_struct_scr.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_mdb_model_struct_src.entity_id' _item.category_id mdb_model_struct_src _item.mandatory_code no _item_type.code code save_ save__mdb_model_struct_src.mod_id _item_description.description ; This data item is a pointer to _mdb_model.id in the MDB_MODEL category. ; _item.name '_mdb_model_struct_src.mod_id' _item.category_id mdb_model_struct_src _item.mandatory_code yes _item_type.code code save_ save__mdb_model_struct_src.align_match _item_description.description ; Flag indicating if the alignment match value was submitted by the author(s) or genereted by MDB. ; _item.name '_mdb_model_struct_src.align_match' _item.category_id mdb_model_struct_src _item.mandatory_code no _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail SD 'submitted data' GD 'generated data' save_ save__mdb_model_struct_src.align_consensus _item_description.description ; Flag indicating if the consensus sequence was submitted by the author(s) or genereted by MDB. ; _item.name '_mdb_model_struct_src.align_consensus' _item.category_id mdb_model_struct_src _item.mandatory_code no _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail SD 'submitted data' GD 'generated data' save_ save__mdb_model_struct_src.align_probability _item_description.description ; Flag indicating if the alignment probability values were submitted by the author(s) or genereted by MDB. ; _item.name '_mdb_model_struct_src.align_probability' _item.category_id mdb_model_struct_src _item.mandatory_code no _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail SD 'submitted data' GD 'generated data' save_ save__mdb_model_struct_src.accuracy_bond_length _item_description.description ; Flag indicating if the bond length accuracy values were submitted by the author(s) or genereted by MDB. ; _item.name '_mdb_model_struct_src.accuracy_bond_length' _item.category_id mdb_model_struct_src _item.mandatory_code no _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail SD 'submitted data' GD 'generated data' save_ save__mdb_model_struct_src.accuracy_bond_angle _item_description.description ; Flag indicating if the bond angle accuracy values were submitted by the author(s) or genereted by MDB. ; _item.name '_mdb_model_struct_src.accuracy_bond_angle' _item.category_id mdb_model_struct_src _item.mandatory_code no _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail SD 'submitted data' GD 'generated