DTD

<?xml version="1.0" encoding="iso-8859-1"?> <!-- ************************************************************* --> <!-- ************************************************************* --> <!-- URI(tm) Universal Research Interchange Format --> <!-- Document Type Definition DTD --> <!-- --> <!-- ************************************************************* --> <!-- This document defines an XML-compliant DTD for the --> <!-- representation and display of protein sequence information. --> <!-- ************************************************************* --> <!-- Author:Jing Zhang --> <!-- date:04/02/2004 --> <!-- ************************************************************* --> <!-- validate here: http://msdn.microsoft.com/downloads/samples/ --> <!-- internet/default.asp?url=/downloads/samples/internet/xml/ --> <!-- xml_validator/default.asp --> <!-- ************************************************************* --> <!-- ************************************************************* --> <!--***************************************************************--> <!-- The root element is URI_protein --> <!--***************************************************************--> <!ELEMENT URI_protein (attributes?,annotation?,seq_data?,sites?,crystal_cell?,orig_matrices?,model_atoms?, connections?,bookkeep_information?)> <!ATTLIST URI_protein pdb_id CDATA #REQUIRED> <!--****************************************************************--> <!--The attributes element includes the content of HEADER,OBSLTE, --> <!--TITLE,CAVEAT,COMPND,SOURCE,KEYWDS,EXPWDS in PDB file --> <!--****************************************************************--> <!ELEMENT attributes (header*,deletion*,titles*,error_warn*,compounds*,sources*,keywords*)> <!ATTLIST attributes pdb_id CDATA #IMPLIED> <!ELEMENT header EMPTY> <!ATTLIST header classification CDATA #IMPLIED> <!ATTLIST header deposition_date CDATA #IMPLIED > <!ATTLIST header pdb_id CDATA #IMPLIED> <!ELEMENT deletion (dele_date*,auth_pdb_id*,replace_pdb_ids* )> <!ELEMENT dele_date (#PCDATA)> <!ELEMENT auth_pdb_id (#PCDATA)><!--auth_pdb_id--> <!ELEMENT replace_pdb_ids (replace_pdb_id*)> <!ELEMENT replace_pdb_id (#PCDATA)> <!ATTLIST replace_pdb_id deletion_entry_id CDATA #REQUIRED ><!--the order num--> <!ELEMENT titles (title*) > <!ATTLIST titles pdb_id CDATA #IMPLIED> <!ELEMENT title (#PCDATA) > <!ATTLIST title title_entry_id CDATA #REQUIRED> <!ELEMENT error_warn (#PCDATA) > <!ATTLIST error_warn pdb_id CDATA #IMPLIED> <!ELEMENT compounds (compound*)> <!ATTLIST compounds pdb_id CDATA #IMPLIED> <!ELEMENT compound (#PCDATA )> <!ATTLIST compound compound_entry_id CDATA #REQUIRED> <!ELEMENT sources (source*)> <!ATTLIST sources pdb_id CDATA #IMPLIED> <!ELEMENT source (#PCDATA)> <!ATTLIST source source_entry_id CDATA #REQUIRED> <!ELEMENT keywords (#PCDATA)> <!ATTLIST keywords pdb_id CDATA #IMPLIED> <!--****************************************************************--> <!--The annotation element includes the content of EXPDTA,AUTHOR --> <!--REVDAT,SPRSDE,JRNL,REMRKS in PDb file --> <!--****************************************************************--> <!ELEMENT annotation (experiment_method*, annotation_authors*,revision_dates*,superseded_entry*,remarks*)> <!ATTLIST annotation pdb_id CDATA #IMPLIED> <!ELEMENT experiment_method (#PCDATA)> <!ATTLIST experiment_method pdb_id CDATA #IMPLIED> <!ELEMENT annotation_authors (author*)> <!ATTLIST annotation_authors pdb_id CDATA #IMPLIED> <!ELEMENT author EMPTY> <!ATTLIST author author_entry_id CDATA #REQUIRED> <!ATTLIST author author_name CDATA #IMPLIED> <!ELEMENT revision_dates (revision_date*)> <!ATTLIST revision_dates pdb_id CDATA #IMPLIED> <!ELEMENT revision_date (revision_record_names*)> <!ATTLIST revision_date revision_date_id CDATA #REQUIRED> <!ATTLIST revision_date revision_date CDATA #IMPLIED> <!ATTLIST revision_date revision_pdb_id CDATA #IMPLIED> <!ATTLIST revision_date revision_type CDATA #IMPLIED> <!ELEMENT revision_record_names (revision_record_name*)> <!ELEMENT revision_record_name EMPTY> <!ATTLIST revision_record_name record_name_entry_id CDATA #REQUIRED> <!ATTLIST revision_record_name record_name CDATA #IMPLIED> <!ELEMENT superseded_entry (superseded_date*, superseded_pdb_ids*)> <!ATTLIST superseded_entry pdb_id CDATA #IMPLIED> <!ELEMENT superseded_date (#PCDATA)> <!ELEMENT superseded_pdb_ids (superseded_pdb_id*)> <!ELEMENT superseded_pdb_id (#PCDATA)> <!ATTLIST superseded_pdb_id supersed_entry_id CDATA #REQUIRED > <!ELEMENT remarks (remark*)> <!ATTLIST remarks pdb_id CDATA #IMPLIED> <!ELEMENT remark (ref_citations*,resolutions*,refinements*,format_versions*,warnings*,other_remarks*)> <!ATTLIST remark pdb_id CDATA #IMPLIED> <!ATTLIST remark remark_id CDATA #REQUIRED> <!ELEMENT ref_citations (ref_citation*)> <!ATTLIST ref_citations remark_id CDATA #FIXED "1"> <!ATTLIST ref_citations remark_type CDATA #FIXED "references" > <!ELEMENT ref_citation (ref_citations_authors*, ref_citations_title*,editors*,to_be_pulished*,journal_abbrev*,journal_vol*,first_page*,year*,publishers*,journal_id_ASTM*,country*,journal_id_ISSN*,journal_id_ISBN*,ccdc_pdb_code*)><!-- remark_id =1--> <!ATTLIST ref_citation remark_id CDATA #FIXED "1"> <!ATTLIST ref_citation citation_id CDATA #REQUIRED><!--primary for JRNL,integer forothers--> <!ATTLIST ref_citation remark_type CDATA #FIXED "references" > <!ELEMENT ref_citations_authors (#PCDATA)> <!ELEMENT ref_citations_title (#PCDATA)> <!ELEMENT editors (#PCDATA)> <!ELEMENT to_be_pulished EMPTY> <!ATTLIST to_be_pulished publish_type CDATA #FIXED "to_be_pulished" > <!ELEMENT journal_abbrev (#PCDATA)> <!ELEMENT journal_vol (#PCDATA)> <!ELEMENT first_page (#PCDATA)> <!ELEMENT year (#PCDATA)> <!ELEMENT publishers (#PCDATA)> <!ELEMENT journal_id_ASTM (#PCDATA)> <!ELEMENT country (#PCDATA)> <!ELEMENT journal_id_ISSN (#PCDATA)> <!ELEMENT journal_id_ISBN (#PCDATA)> <!ELEMENT ccdc_pdb_code (#PCDATA)><!--could be 0530 for unpub or others--> <!ELEMENT resolutions (resolution*)><!-- remark_id =2--> <!ATTLIST resolutions pdb_id CDATA #IMPLIED> <!ATTLIST resolutions remark_id CDATA #FIXED "2"> <!ATTLIST resolutions remark_type CDATA #FIXED "resolution" > <!ELEMENT resolution (resolution_value*,angstorms*,resolution_detail*)> <!ATTLIST resolution resolution_id CDATA #IMPLIED><!--the order num--> <!ATTLIST resolution resolution_no_applicable (True|False) "False" > <!ELEMENT resolution_value (#PCDATA)> <!ELEMENT angstorms (#PCDATA)> <!ELEMENT resolution_detail (#PCDATA)> <!ELEMENT refinements (refinement*)><!-- remark_id =3--> <!ATTLIST refinements pdb_id CDATA #IMPLIED> <!ATTLIST refinements remark_id CDATA #FIXED "3"> <!ATTLIST refinements remark_type CDATA #FIXED "refinements" > <!ELEMENT refinement (diffraction_data*,no_diffraction_data*)> <!ATTLIST refinement refinement_entry_id CDATA #REQUIRED> <!ATTLIST refinement refinement_type (DIFFRACTION|NON-DIFFRACTION) #IMPLIED> <!ELEMENT diffraction_data (diff_refinement_authors*,data_used*,fit_to_data_used*,fit_highest_resolution*,fit_agree_mod?,num_non-hydro_atom*,wilson_b_val_fcalc*,b_value*,estimated_coordinate_error*,cv_coordinate_error*,mod_refinements*,rms_deviation*,incorrect_chiral_center_count*,bulk_solvent_mod*,res_library*,stereochem_target_val*,isotropic_therm_mod*,isotropic_therm_restraints*,ncs_mod*,ncs_restraints*,parameter_files*,topology_files*,other_refinement*)> <!ATTLIST diffraction_data refinement_entry_id CDATA #REQUIRED> <!ATTLIST diffraction_data refinement_type (X-PLOR|NUCLSQ|PROLSQ|CCP4|PROFFT|GPRLSA|SHELXL|TNT) #IMPLIED> <!ELEMENT diff_refinement_authors (#PCDATA)> <!ELEMENT data_used (high_resolution*,low_resolution*,data_cutoff*,cutoff_high*,cutoff_low*,completeness*,num_reflections*,cross_v_method*,data_free_r_test*)> <!ATTLIST data_used refinement_type (X-PLOR|NUCLSQ|PROLSQ|CCP4|PROFFT|GPRLSA|SHELXL|TNT) #IMPLIED> <!ATTLIST data_used refinement_entry_id CDATA #REQUIRED> <!ELEMENT high_resolution (#PCDATA)> <!ELEMENT low_resolution (#PCDATA)> <!ELEMENT data_cutoff (#PCDATA)> <!ELEMENT cutoff_high (#PCDATA)> <!ELEMENT cutoff_low (#PCDATA)> <!ELEMENT completeness (#PCDATA)> <!ELEMENT num_reflections (#PCDATA)> <!ELEMENT cross_v_method (#PCDATA)> <!ELEMENT data_free_r_test (#PCDATA)> <!ELEMENT fit_to_data_used (cv_method*,free_r_value_selection*,r_value_work_test*,r_value_work*,free_r_value*,free_r_value_size*,free_r_value_count*,free_r_value_error*,fit_num_reflection*)> <!ATTLIST fit_to_data_used refinement_type (X-PLOR|NUCLSQ|PROLSQ|CCP4|PROFFT|GPRLSA|SHELXL|TNT) #IMPLIED> <!ATTLIST fit_to_data_used refinement_entry_id CDATA #REQUIRED> <!ATTLIST fit_to_data_used fit_to_data_used_type (fit_data|data_above_sigma_cutoff|data_all_no_sigma_cutoff) #REQUIRED> <!--fit_data for x-plor,others for tnt--> <!ELEMENT cv_method (#PCDATA)> <!ELEMENT free_r_value_selection (#PCDATA)> <!ELEMENT r_value_work_test (#PCDATA)> <!ELEMENT r_value_work (#PCDATA)> <!ELEMENT free_r_value (#PCDATA)> <!ELEMENT free_r_value_size (#PCDATA)> <!ELEMENT free_r_value_count (#PCDATA)> <!ELEMENT free_r_value_error (#PCDATA)> <!ELEMENT fit_num_reflection (#PCDATA)> <!ELEMENT fit_highest_resolution (num_bins*,bin_high_resolution*,bin_low_resolution*,bin_completeness*,bin_reflections*,bin_r_value*,bin_free_r_value*,bin_free_r_value_size*,bin_free_r_value_count*,bin_free_r_value_error*)> <!ATTLIST fit_highest_resolution refinement_type (X-PLOR|NUCLSQ|PROLSQ|CCP4|PROFFT|GPRLSA|SHELXL|TNT) #IMPLIED> <!ATTLIST fit_highest_resolution refinement_entry_id CDATA #REQUIRED> <!ELEMENT num_bins (#PCDATA)> <!ELEMENT bin_high_resolution (#PCDATA)> <!ELEMENT bin_low_resolution (#PCDATA)> <!ELEMENT bin_completeness (#PCDATA)> <!ELEMENT bin_reflections (#PCDATA)> <!ELEMENT bin_r_value (#PCDATA)> <!ELEMENT bin_free_r_value (#PCDATA)> <!ELEMENT bin_free_r_value_size (#PCDATA)> <!ELEMENT bin_free_r_value_count (#PCDATA)> <!ELEMENT bin_free_r_value_error (#PCDATA)> <!ELEMENT fit_agree_mod (agree_r_value_work_test*,agree_r_value_work*,agree_free_r_value*,agree_free_r_value_size*,agree_free_r_value_count*,agree_num_reflection*)> <!ATTLIST fit_agree_mod refinement_type (X-PLOR|NUCLSQ|PROLSQ|CCP4|PROFFT|GPRLSA|SHELXL|TNT) #IMPLIED> <!ATTLIST fit_agree_mod refinement_entry_id CDATA #REQUIRED> <!ATTLIST fit_agree_mod agree_data_type (all|F_gt_4SIG) "all"> <!ELEMENT agree_r_value_work_test (#PCDATA)> <!ELEMENT agree_r_value_work (#PCDATA)> <!ELEMENT agree_free_r_value (#PCDATA)> <!ELEMENT agree_free_r_value_size (#PCDATA)> <!ELEMENT agree_free_r_value_count (#PCDATA)> <!ELEMENT agree_num_reflection (#PCDATA)> <!ELEMENT num_non-hydro_atom (non_hydro_protein_atom*,non_hydro_nucleic_atom*,non_hydro_heterogen_atom*,non_hydro_solvent_atom*,non_hydro_other_atom*)> <!ATTLIST num_non-hydro_atom refinement_type (X-PLOR|NUCLSQ|PROLSQ|CCP4|PROFFT|GPRLSA|SHELXL|TNT) #IMPLIED> <!ATTLIST num_non-hydro_atom refinement_entry_id CDATA #REQUIRED> <!ELEMENT non_hydro_protein_atom (#PCDATA)> <!ELEMENT non_hydro_nucleic_atom (#PCDATA)> <!ELEMENT non_hydro_heterogen_atom (#PCDATA)> <!ELEMENT non_hydro_solvent_atom (#PCDATA)> <!ELEMENT non_hydro_other_atom (#PCDATA)> <!ELEMENT wilson_b_val_fcalc (#PCDATA)> <!ELEMENT b_value (wilson_plot*,mean_b_value*,anisotropic_b_values*)> <!ATTLIST b_value refinement_type (X-PLOR|NUCLSQ|PROLSQ|CCP4|PROFFT|GPRLSA|SHELXL|TNT) #IMPLIED> <!ATTLIST b_value refinement_entry_id CDATA #REQUIRED> <!ELEMENT wilson_plot (#PCDATA)> <!ELEMENT mean_b_value (#PCDATA)> <!ELEMENT anisotropic_b_values (b11*,b22*,b33*,b12*,b13*,b23*)> <!ELEMENT b11 (#PCDATA)> <!ELEMENT b22 (#PCDATA)> <!ELEMENT b33 (#PCDATA)> <!ELEMENT b12 (#PCDATA)> <!ELEMENT b13 (#PCDATA)> <!ELEMENT b23 (#PCDATA)> <!ELEMENT estimated_coordinate_error (esd_luzzati_plot*,esd_sigmaa*,esd_low_resolutin_cutoff*)> <!ATTLIST estimated_coordinate_error refinement_type (X-PLOR|NUCLSQ|PROLSQ|CCP4|PROFFT|GPRLSA|SHELXL|TNT) #IMPLIED> <!ATTLIST estimated_coordinate_error refinement_entry_id CDATA #REQUIRED> <!ELEMENT esd_luzzati_plot (#PCDATA)> <!ELEMENT esd_sigmaa (#PCDATA)> <!ELEMENT esd_low_resolutin_cutoff (#PCDATA)> <!ELEMENT cv_coordinate_error (esd_cv_luzzati_plot*,esd_cv_sigmaa*)> <!ATTLIST cv_coordinate_error refinement_type (X-PLOR|NUCLSQ|PROLSQ|CCP4|PROFFT|GPRLSA|SHELXL|TNT) #IMPLIED> <!ATTLIST cv_coordinate_error refinement_entry_id CDATA #REQUIRED> <!ELEMENT esd_cv_luzzati_plot (#PCDATA)> <!ELEMENT esd_cv_sigmaa (#PCDATA)> <!--for shelxl--> <!ELEMENT mod_refinements (occup_sum_non_hydro*,occup_sum_hydro*,num_disorder_resd*,num_least_squa_para*,num_restaints*)> <!ATTLIST mod_refinements refinement_type (X-PLOR|NUCLSQ|PROLSQ|CCP4|PROFFT|GPRLSA|SHELXL|TNT) #IMPLIED> <!ATTLIST mod_refinements refinement_entry_id CDATA #REQUIRED> <!ELEMENT occup_sum_non_hydro (#PCDATA)> <!ELEMENT occup_sum_hydro (#PCDATA)> <!ELEMENT num_disorder_resd (#PCDATA)> <!ELEMENT num_least_squa_para (#PCDATA)> <!ELEMENT num_restaints (#PCDATA)> <!ELEMENT rms_deviation (rms_bond_length*,rms_bond_angl*,rms_dihedral_angl*,rms_improper_angl*,dis_restraints*,plane_restraints*,c-center_restraints*,non-bonded_restraints*,conf_torsion_ang_restraints*,angle_distances*,similar_dis_no_target_value*,dis_restraint_plane*,zero_chiral_vol*,non_zero_chiral_vol*,anti_bump_dis*,rigid_bond_adp*,similar_adp*,isotropic_adp*,torsion_angles*,pseudo_rota_ang*,tri_carbon_plane*,general_plane*,isotrop_thermal_factors*,non_bonded_contacts*)> <!ATTLIST rms_deviation refinement_type (X-PLOR|NUCLSQ|PROLSQ|CCP4|PROFFT|GPRLSA|SHELXL|TNT) #IMPLIED> <!ATTLIST rms_deviation refinement_entry_id CDATA #REQUIRED> <!ATTLIST rms_deviation rms_deviation_type (IDEAL_VALUE|RESTRAINT_TARGET_VALUE) #REQUIRED> <!--for x-plor--> <!ELEMENT rms_bond_length ANY> <!--for tnt, not content but there attr. for x-por and shelxl, CDATAcontent, no attr --> <!ATTLIST rms_bond_length rms CDATA #IMPLIED> <!ATTLIST rms_bond_length sigma CDATA #IMPLIED> <!ATTLIST rms_bond_length count CDATA #IMPLIED> <!--for tnt, not content but there attr. for x-por , CDATAcontent, no attr --> <!ELEMENT rms_bond_angl ANY> <!ATTLIST rms_bond_angl rms CDATA #IMPLIED> <!ATTLIST rms_bond_angl sigma CDATA #IMPLIED> <!ATTLIST rms_bond_angl count CDATA #IMPLIED> <!ELEMENT rms_dihedral_angl (#PCDATA)> <!ELEMENT rms_improper_angl (#PCDATA)> <!--for nuclsq and pro.ccp4,profft,gpr--> <!ELEMENT dis_restraints (sugar_bond_dis*,sugar_bond_ang_dis*,phosphate_bond_dis*,phosphate_bond_ang_dis_h_bond*,bond_length*,ang_dis*,intraplanar_1_4_dis*,h_bond_metal_coordination*)> <!ELEMENT sugar_bond_dis EMPTY> <!ATTLIST sugar_bond_dis rms CDATA #IMPLIED> <!ATTLIST sugar_bond_dis sigma CDATA #IMPLIED> <!ELEMENT sugar_bond_ang_dis EMPTY > <!ATTLIST sugar_bond_ang_dis rms CDATA #IMPLIED> <!ATTLIST sugar_bond_ang_dis sigma CDATA #IMPLIED> <!ELEMENT phosphate_bond_dis EMPTY> <!ATTLIST phosphate_bond_dis rms CDATA #IMPLIED> <!ATTLIST phosphate_bond_dis sigma CDATA #IMPLIED> <!ELEMENT phosphate_bond_ang_dis_h_bond EMPTY > <!ATTLIST phosphate_bond_ang_dis_h_bond rms CDATA #IMPLIED> <!ATTLIST phosphate_bond_ang_dis_h_bond sigma CDATA #IMPLIED> <!ELEMENT bond_length EMPTY> <!ATTLIST bond_length rms CDATA #IMPLIED> <!ATTLIST bond_length sigma CDATA #IMPLIED> <!ELEMENT ang_dis EMPTY> <!ATTLIST ang_dis rms CDATA #IMPLIED> <!ATTLIST ang_dis sigma CDATA #IMPLIED> <!ELEMENT intraplanar_1_4_dis EMPTY> <!ATTLIST intraplanar_1_4_dis rms CDATA #IMPLIED> <!ATTLIST intraplanar_1_4_dis sigma CDATA #IMPLIED> <!ELEMENT h_bond_metal_coordination EMPTY> <!ATTLIST h_bond_metal_coordination rms CDATA #IMPLIED> <!ATTLIST h_bond_metal_coordination sigma CDATA #IMPLIED> <!ELEMENT plane_restraints EMPTY> <!ATTLIST plane_restraints rms CDATA #IMPLIED> <!ATTLIST plane_restraints sigma CDATA #IMPLIED> <!ELEMENT c-center_restraints EMPTY> <!ATTLIST c-center_restraints rms CDATA #IMPLIED> <!ATTLIST c-center_restraints sigma CDATA #IMPLIED> <!ELEMENT non-bonded_restraints (single_torsion_contact*,multi_torsion_contact*,single_torsion*,multi_torsion*,h_bond_xy*,h_bond_xhy*)> <!ELEMENT single_torsion_contact EMPTY> <!ATTLIST single_torsion_contact rms CDATA #IMPLIED> <!ATTLIST single_torsion_contact sigma CDATA #IMPLIED> <!ELEMENT multi_torsion_contact EMPTY> <!ATTLIST multi_torsion_contact rms CDATA #IMPLIED> <!ATTLIST multi_torsion_contact sigma CDATA #IMPLIED> <!ELEMENT single_torsion EMPTY> <!ATTLIST single_torsion rms CDATA #IMPLIED> <!ATTLIST single_torsion sigma CDATA #IMPLIED> <!ELEMENT multi_torsion EMPTY> <!ATTLIST multi_torsion rms CDATA #IMPLIED> <!ATTLIST multi_torsion sigma CDATA #IMPLIED> <!ELEMENT h_bond_xy EMPTY> <!ATTLIST h_bond_xy rms CDATA #IMPLIED> <!ATTLIST h_bond_xy sigma CDATA #IMPLIED> <!ELEMENT h_bond_xhy EMPTY> <!ATTLIST h_bond_xhy rms CDATA #IMPLIED> <!ATTLIST h_bond_xhy sigma CDATA #IMPLIED> <!--for pro.ccp4,profft,gpr--> <!ELEMENT conf_torsion_ang_restraints (specified_degree*,planar_degree*,staggered_degree*,transverse_degree*)> <!ELEMENT specified_degree EMPTY> <!ATTLIST specified_degree rms CDATA #IMPLIED> <!ATTLIST specified_degree sigma CDATA #IMPLIED> <!ELEMENT planar_degree EMPTY> <!ATTLIST planar_degree rms CDATA #IMPLIED> <!ATTLIST planar_degree sigma CDATA #IMPLIED> <!ELEMENT staggered_degree EMPTY> <!ATTLIST staggered_degree rms CDATA #IMPLIED> <!ATTLIST staggered_degree sigma CDATA #IMPLIED> <!ELEMENT transverse_degree EMPTY> <!ATTLIST transverse_degree rms CDATA #IMPLIED> <!ATTLIST transverse_degree sigma CDATA #IMPLIED> <!--for shelxl--> <!ELEMENT angle_distances (#PCDATA)> <!ELEMENT similar_dis_no_target_value (#PCDATA)> <!ELEMENT dis_restraint_plane (#PCDATA)> <!ELEMENT zero_chiral_vol (#PCDATA)> <!ELEMENT non_zero_chiral_vol (#PCDATA)> <!ELEMENT anti_bump_dis (#PCDATA)> <!ELEMENT rigid_bond_adp (#PCDATA)> <!ELEMENT similar_adp (#PCDATA)> <!ELEMENT isotropic_adp (#PCDATA)> <!--for tnt--> <!ELEMENT torsion_angles EMPTY> <!ATTLIST torsion_angles rms CDATA #IMPLIED> <!ATTLIST torsion_angles sigma CDATA #IMPLIED> <!ATTLIST torsion_angles count CDATA #IMPLIED> <!ELEMENT pseudo_rota_ang EMPTY> <!ATTLIST pseudo_rota_ang rms CDATA #IMPLIED> <!ATTLIST pseudo_rota_ang sigma CDATA #IMPLIED> <!ATTLIST pseudo_rota_ang count CDATA #IMPLIED> <!ELEMENT tri_carbon_plane EMPTY> <!ATTLIST tri_carbon_plane rms CDATA #IMPLIED> <!ATTLIST tri_carbon_plane sigma CDATA #IMPLIED> <!ATTLIST tri_carbon_plane count CDATA #IMPLIED> <!ELEMENT general_plane EMPTY> <!ATTLIST general_plane rms CDATA #IMPLIED> <!ATTLIST general_plane sigma CDATA #IMPLIED> <!ATTLIST general_plane count CDATA #IMPLIED> <!ELEMENT isotrop_thermal_factors EMPTY> <!ATTLIST isotrop_thermal_factors rms CDATA #IMPLIED> <!ATTLIST isotrop_thermal_factors sigma CDATA #IMPLIED> <!ATTLIST isotrop_thermal_factors count CDATA #IMPLIED> <!ELEMENT non_bonded_contacts EMPTY> <!ATTLIST non_bonded_contacts rms CDATA #IMPLIED> <!ATTLIST non_bonded_contacts sigma CDATA #IMPLIED> <!ATTLIST non_bonded_contacts count CDATA #IMPLIED> <!ELEMENT incorrect_chiral_center_count (#PCDATA)> <!ELEMENT bulk_solvent_mod (method_used*,ksol*,bsol*)> <!ATTLIST bulk_solvent_mod refinement_type (X-PLOR|NUCLSQ|PROLSQ|CCP4|PROFFT|GPRLSA|SHELXL|TNT) #IMPLIED> <!ATTLIST bulk_solvent_mod refinement_entry_id CDATA #REQUIRED> <!ELEMENT method_used (#PCDATA)> <!ELEMENT ksol (#PCDATA)> <!ELEMENT bsol (#PCDATA)> <!ELEMENT res_library (stereochemistry*,iso_thermal_restraints*)> <!ATTLIST res_library refinement_type (X-PLOR|NUCLSQ|PROLSQ|CCP4|PROFFT|GPRLSA|SHELXL|TNT) #IMPLIED> <!ATTLIST res_library refinement_entry_id CDATA #REQUIRED> <!ELEMENT stereochemistry (#PCDATA)> <!ELEMENT iso_thermal_restraints (#PCDATA)> <!ELEMENT stereochem_target_val (target_val*,special_case*)> <!ATTLIST stereochem_target_val refinement_type (X-PLOR|NUCLSQ|PROLSQ|CCP4|PROFFT|GPRLSA|SHELXL|TNT) #IMPLIED> <!ATTLIST stereochem_target_val refinement_entry_id CDATA #REQUIRED> <!ELEMENT target_val (#PCDATA)> <!ELEMENT special_case (#PCDATA)> <!ELEMENT isotropic_therm_mod (#PCDATA)> <!ELEMENT isotropic_therm_restraints (main_chain_bond*,main_chain_ang*,side_chain_bond*,side_chain_ang*,sugar_bond*,sugar_bond_ang*,phosphate_bond*,phosphate_bond_ang_h_bond*)> <!ATTLIST isotropic_therm_restraints refinement_type (X-PLOR|NUCLSQ|PROLSQ|CCP4|PROFFT|GPRLSA|SHELXL|TNT) #IMPLIED> <!ATTLIST isotropic_therm_restraints refinement_entry_id CDATA #REQUIRED> <!ELEMENT main_chain_bond EMPTY > <!ATTLIST main_chain_bond rms CDATA #IMPLIED> <!ATTLIST main_chain_bond sigma CDATA #IMPLIED> <!ELEMENT main_chain_ang EMPTY > <!ATTLIST main_chain_ang rms CDATA #IMPLIED> <!ATTLIST main_chain_ang sigma CDATA #IMPLIED> <!ELEMENT side_chain_bond EMPTY > <!ATTLIST side_chain_bond rms CDATA #IMPLIED> <!ATTLIST side_chain_bond sigma CDATA #IMPLIED> <!ELEMENT side_chain_ang EMPTY> <!ATTLIST side_chain_ang rms CDATA #IMPLIED> <!ATTLIST side_chain_ang sigma CDATA #IMPLIED> <!-- for NUCLSQ--> <!ELEMENT sugar_bond EMPTY> <!ATTLIST sugar_bond rms CDATA #IMPLIED> <!ATTLIST sugar_bond sigma CDATA #IMPLIED> <!ELEMENT sugar_bond_ang EMPTY> <!ATTLIST sugar_bond_ang rms CDATA #IMPLIED> <!ATTLIST sugar_bond_ang sigma CDATA #IMPLIED> <!ELEMENT phosphate_bond EMPTY> <!ATTLIST phosphate_bond rms CDATA #IMPLIED> <!ATTLIST phosphate_bond sigma CDATA #IMPLIED> <!ELEMENT phosphate_bond_ang_h_bond EMPTY> <!ATTLIST phosphate_bond_ang_h_bond rms CDATA #IMPLIED> <!ATTLIST phosphate_bond_ang_h_bond sigma CDATA #IMPLIED> <!ELEMENT ncs_mod (#PCDATA)> <!ELEMENT ncs_restraints (groups*)> <!ATTLIST ncs_restraints refinement_type (X-PLOR|NUCLSQ|PROLSQ|CCP4|PROFFT|GPRLSA|SHELXL|TNT) #IMPLIED> <!ATTLIST ncs_restraints refinement_entry_id CDATA #REQUIRED> <!ELEMENT groups (group*)> <!ELEMENT group (positional?,b_factor?)> <!ATTLIST group group_entry_id (1|2|3|4) #REQUIRED> <!ELEMENT positional EMPTY > <!ATTLIST positional rms CDATA #IMPLIED> <!ATTLIST positional sigma_weight CDATA #IMPLIED> <!ELEMENT b_factor EMPTY> <!ATTLIST b_factor rms CDATA #IMPLIED> <!ATTLIST b_factor sigma_weight CDATA #IMPLIED> <!ELEMENT parameter_files (parameter_file*)> <!ATTLIST parameter_files refinement_type (X-PLOR|NUCLSQ|PROLSQ|CCP4|PROFFT|GPRLSA|SHELXL|TNT) #IMPLIED> <!ATTLIST parameter_files refinement_entry_id CDATA #REQUIRED> <!ELEMENT parameter_file (#PCDATA)> <!ATTLIST parameter_file parameter_file_entry_id (1|2|3|4|5|6) #REQUIRED> <!ELEMENT topology_files (topology_file*)> <!ATTLIST topology_files refinement_type (X-PLOR|NUCLSQ|PROLSQ|CCP4|PROFFT|GPRLSA|SHELXL|TNT) #IMPLIED> <!ATTLIST topology_files refinement_entry_id CDATA #REQUIRED> <!ELEMENT topology_file (#PCDATA)> <!ATTLIST topology_file topology_file_entry_id (1|2|3|4|5|6) #REQUIRED> <!ELEMENT other_refinement (#PCDATA)> <!ATTLIST other_refinement refinement_type (X-PLOR|NUCLSQ|PROLSQ|CCP4|PROFFT|GPRLSA|SHELXL|TNT) #IMPLIED> <!ATTLIST other_refinement refinement_entry_id CDATA #REQUIRED> <!ELEMENT no_diffraction_data (no_diffra_prog*,no_diffra_author*,no_diffra_details*)> <!ATTLIST no_diffraction_data refinement_type CDATA #FIXED "NON-DIFFRACTION"> <!ATTLIST no_diffraction_data refinement_entry_id CDATA #REQUIRED> <!ELEMENT no_diffra_prog (#PCDATA)> <!ELEMENT no_diffra_author (#PCDATA)> <!ELEMENT no_diffra_details (#PCDATA)> <!--end of remark_id=3--> <!ELEMENT format_versions (format_version*)><!-- remark_id =4 --> <!ATTLIST format_versions pdb_id CDATA #IMPLIED> <!ATTLIST format_versions remark_id CDATA #FIXED "4"> <!ATTLIST format_versions remark_type CDATA #FIXED "format_version"> <!ELEMENT format_version (#PCDATA)> <!ATTLIST format_version format_version_entry_id CDATA #REQUIRED> <!ATTLIST format_version format_version_num CDATA #IMPLIED> <!ATTLIST format_version format_version_date CDATA #IMPLIED> <!--end of remark_id=4--> <!ELEMENT warnings (warning*)><!-- remark_id =5 --> <!ATTLIST warnings pdb_id CDATA #IMPLIED> <!ATTLIST warnings remark_id CDATA #FIXED "5"> <!ATTLIST warnings remark_type CDATA #FIXED "warnings"> <!ELEMENT warning (#PCDATA)> <!ATTLIST warning warning_entry_id CDATA #REQUIRED> <!--end of remark_id=5--> <!ELEMENT other_remarks (other_remark*)><!-- remark_id >=100--> <!ATTLIST other_remarks pdb_id CDATA #IMPLIED> <!ATTLIST other_remarks remark_id CDATA #IMPLIED> <!ATTLIST other_remarks remark_type CDATA #FIXED "others" > <!ELEMENT other_remark (#PCDATA)><!-- remark_id >=100--> <!ATTLIST other_remark other_remark_entry_id CDATA #REQUIRED> <!ATTLIST other_remark pdb_id CDATA #IMPLIED> <!ATTLIST other_remark remark_id CDATA #IMPLIED> <!ATTLIST other_remark remark_type CDATA #FIXED "others" > <!--***************************************************************--> <!--The seq_data element includes the content of primary --> <!--structure(DBREF,SEDADV,SEQRES,MODRES), heterogen section(HET, --> <!--HETNAM,HETSYN,FORMUL),secondary structure(HELIX,SHEET,TURN), --> <!--connectivity annotation(SSBOND,LINK,SLTBRG,CISPEP) --> <!--***************************************************************--> <!ELEMENT seq_data (struct_refs*,sequences*,modification_resds*,non-polyer_seqs*,struct_helixes*,struct_sheets*,struct_turns*,bonds*,protein_cis_es*)> <!ATTLIST seq_data pdb_id CDATA #IMPLIED> <!ELEMENT struct_refs (db_struct_refs*, struct_refs_seq_difs*)> <!ATTLIST struct_refs pdb_id CDATA #IMPLIED> <!ELEMENT db_struct_refs (db_struct_ref*)> <!ATTLIST db_struct_refs pdb_id CDATA #IMPLIED> <!ELEMENT db_struct_ref (db_struct_ref_pdb_id*, db_struct_ref_seq_type*,db_struct_ref_seq_align_begin*,db_struct_ref_insertion_begin*,db_struct_ref_seq_align_end*, db_struct_ref_insertion_end*,db_struct_ref_db_name*,db_struct_ref_db_accession*,db_struct_ref_db_code*,db_struct_ref_auth_align_begin*,db_struct_ref_auth_insertion_begin*,db_struct_ref_auth_align_end*,db_struct_ref_auth_insertion_end*)> <!ATTLIST db_struct_ref db_struct_ref_id CDATA #REQUIRED ><!--the order num--> <!ELEMENT db_struct_ref_pdb_id (#PCDATA)> <!ELEMENT db_struct_ref_seq_type (#PCDATA)> <!ELEMENT db_struct_ref_seq_align_begin (#PCDATA)> <!ELEMENT db_struct_ref_insertion_begin (#PCDATA)> <!ELEMENT db_struct_ref_seq_align_end (#PCDATA)> <!ELEMENT db_struct_ref_insertion_end (#PCDATA)> <!ELEMENT db_struct_ref_db_name (#PCDATA)> <!ELEMENT db_struct_ref_db_accession (#PCDATA)> <!ELEMENT db_struct_ref_db_code (#PCDATA)> <!ELEMENT db_struct_ref_auth_align_begin (#PCDATA)> <!ELEMENT db_struct_ref_auth_insertion_begin (#PCDATA)> <!ELEMENT db_struct_ref_auth_align_end (#PCDATA)> <!ELEMENT db_struct_ref_auth_insertion_end (#PCDATA)> <!ELEMENT struct_refs_seq_difs (struct_ref_seq_dif*)> <!ATTLIST struct_refs_seq_difs pdb_id CDATA #IMPLIED> <!ELEMENT struct_ref_seq_dif (struct_ref_seq_pdb_id*, struct_ref_seq_aminoacid_id*, struct_ref_seq_pdb_strand_id*, struct_ref_seq_db_name*, struct_ref_seq_db_accession*, struct_ref_seq_details*)> <!ATTLIST struct_ref_seq_dif struct_ref_seq_dif_id CDATA #REQUIRED > <!ATTLIST struct_ref_seq_dif seq_num CDATA #IMPLIED > <!ELEMENT struct_ref_seq_pdb_id (#PCDATA)> <!ELEMENT struct_ref_seq_aminoacid_id (#PCDATA)> <!ELEMENT struct_ref_seq_pdb_strand_id (#PCDATA)> <!ELEMENT struct_ref_seq_db_name (#PCDATA)> <!ELEMENT struct_ref_seq_db_accession (#PCDATA)> <!ELEMENT struct_ref_seq_details (#PCDATA)> <!ELEMENT sequences (sequence*,footnotes*)> <!ATTLIST sequences pdb_id CDATA #IMPLIED> <!ELEMENT sequence (wholesequence*,seq_residues*)> <!ATTLIST sequence seq_id CDATA #REQUIRED> <!ATTLIST sequence seq_type CDATA #IMPLIED ><!--chaintype--> <!ATTLIST sequence num_resds CDATA #IMPLIED > <!ELEMENT wholesequence (one_letter_seq*, three_letter_seq*)> <!ATTLIST wholesequence seq_id CDATA #IMPLIED > <!ATTLIST wholesequence seq_type CDATA #IMPLIED > <!ELEMENT one_letter_seq (#PCDATA)> <!ATTLIST one_letter_seq seq_id CDATA #IMPLIED> <!ELEMENT three_letter_seq (#PCDATA)> <!ATTLIST three_letter_seq seq_id CDATA #IMPLIED> <!ELEMENT seq_residues (seq_residue*)> <!ATTLIST seq_residues seq_id CDATA #IMPLIED > <!ATTLIST seq_residues seq_type CDATA #IMPLIED > <!ATTLIST seq_residues num_resds CDATA #IMPLIED > <!ELEMENT seq_residue (residue_name*,one_letter_name*,three_letter_name*, phi_angle*,psi_angle*,residue_weight*, residue_formula*,hydrophobicity_scale*)> <!ATTLIST seq_residue residue_id CDATA #REQUIRED><!--# order num--> <!ATTLIST seq_residue seq_id CDATA #IMPLIED > <!ATTLIST seq_residue seq_type CDATA #IMPLIED > <!ATTLIST seq_residue num_resds CDATA #IMPLIED > <!ELEMENT residue_name (#PCDATA ) ><!--# original name--> <!ELEMENT one_letter_name (#PCDATA )><!--#1letter--> <!ELEMENT three_letter_name (#PCDATA ) > <!--#3letter--> <!ELEMENT phi_angle (#PCDATA )><!--phi--> <!ELEMENT psi_angle (#PCDATA )><!--psi--> <!ELEMENT residue_weight (#PCDATA)><!--which one--> <!ELEMENT residue_formula (#PCDATA)> <!ELEMENT hydrophobicity_scale (#PCDATA) > <!--type--> <!ATTLIST hydrophobicity_scale hydro_type CDATA #IMPLIED> <!ELEMENT footnotes (footnote*)> <!ATTLIST footnotes pdb_id CDATA #IMPLIED> <!ELEMENT footnote (#PCDATA)> <!ATTLIST footnote footnote_id CDATA #REQUIRED > <!ELEMENT modification_resds ( modification_resd*)> <!ATTLIST modification_resds pdb_id CDATA #IMPLIED> <!ELEMENT modification_resd (modification_current_resds*,modification_seq_type*,modification_seq_id*, modification_insertion_code*,modification_standard_resds*, modification_details*)> <!ATTLIST modification_resd entry_id CDATA #REQUIRED> <!ELEMENT modification_current_resds (#PCDATA)> <!ELEMENT modification_seq_type (#PCDATA)> <!ELEMENT modification_seq_id (#PCDATA)> <!ELEMENT modification_insertion_code (#PCDATA)> <!ELEMENT modification_standard_resds (#PCDATA)> <!ELEMENT modification_details (#PCDATA)> <!--non-polyer_seqs--> <!ELEMENT non-polyer_seqs (hets?,hetnams?,hetsyns?,formuls?)> <!ATTLIST non-polyer_seqs pdb_id CDATA #IMPLIED> <!ELEMENT hets (het*)> <!ATTLIST hets non-polyer_seqs_type CDATA #FIXED "HET"> <!ELEMENT het (pdb_het_id?,het_asym_id?,het_seq_id?,het_insertion_code?,het_num_hetatoms?,het_details?)> <!ATTLIST het het_entry_id CDATA #REQUIRED><!--1,2,3--> <!ELEMENT pdb_het_id (#PCDATA) > <!ELEMENT het_asym_id (#PCDATA) > <!ELEMENT het_seq_id (#PCDATA) > <!ELEMENT het_insertion_code (#PCDATA) > <!ELEMENT het_num_hetatoms (#PCDATA) > <!ELEMENT het_details (#PCDATA) > <!ELEMENT hetnams (hetnam*)> <!ATTLIST hetnams non-polyer_seqs_type CDATA #FIXED "HETNAM"> <!ELEMENT hetnam (pdb_hetnam_id?,hetnam_details?)> <!ATTLIST hetnam hetnam_entry_id CDATA #REQUIRED><!--order num--> <!ELEMENT pdb_hetnam_id (#PCDATA) > <!ELEMENT hetnam_details (#PCDATA) > <!ELEMENT hetsyns (hetsyn*)> <!ATTLIST hetsyns non-polyer_seqs_type CDATA #FIXED "HETSYN"> <!ELEMENT hetsyn (pdb_hetsyn_id?,hetsyn_details?)> <!ATTLIST hetsyn hetsyn_entry_id CDATA #REQUIRED><!--order num--> <!ELEMENT pdb_hetsyn_id (#PCDATA) > <!ELEMENT hetsyn_details (#PCDATA) > <!ELEMENT formuls (formul*)> <!ATTLIST formuls non-polyer_seqs_type CDATA #FIXED "FORMUL"> <!ELEMENT formul (for_num_component?,for_het_id?,for_details?)> <!ATTLIST formul formul_entry_id CDATA #REQUIRED><!--order num--> <!ATTLIST formul is_water (True|False) "False" > <!ELEMENT for_num_component (#PCDATA) > <!ELEMENT for_het_id (#PCDATA) > <!ELEMENT for_details (#PCDATA) > <!--end of non-poly--> <!ELEMENT struct_helixes (struct_helix*)> <!ATTLIST struct_helixes pdb_id CDATA #IMPLIED> <!ELEMENT struct_helix (pdb_helix_id*, helix_begin_acid_id*, helix_begin_asym_id*, helix_begin_seq_id*, helix_end_acid_id*, helix_end_asym_id*, helix_end_seq_id*,helix_class*, struct_helix_details*,helix_length*)> <!ATTLIST struct_helix struct_helix_id CDATA #REQUIRED><!--order num--> <!ELEMENT pdb_helix_id (#PCDATA)> <!ELEMENT helix_begin_acid_id (#PCDATA)> <!ELEMENT helix_begin_asym_id (#PCDATA)> <!ELEMENT helix_begin_seq_id (#PCDATA)> <!ELEMENT helix_end_acid_id (#PCDATA)> <!ELEMENT helix_end_asym_id (#PCDATA)> <!ELEMENT helix_end_seq_id (#PCDATA)> <!ELEMENT helix_class (#PCDATA)> <!ELEMENT struct_helix_details (#PCDATA)> <!ELEMENT helix_length (#PCDATA)> <!ELEMENT struct_sheets (struct_sheet*)> <!ATTLIST struct_sheets pdb_id CDATA #IMPLIED> <!ELEMENT struct_sheet (struct_sheet_num_strands*,struct_sheet_order*, struct_sheet_range*, struct_sheet_hbond*)> <!ATTLIST struct_sheet struct_sheet_id CDATA #REQUIRED > <!ELEMENT struct_sheet_num_strands (#PCDATA)> <!ATTLIST struct_sheet_num_strands struct_sheet_id CDATA #IMPLIED> <!ELEMENT struct_sheet_order (sense*)> <!ATTLIST struct_sheet_order struct_sheet_id CDATA #IMPLIED> <!ATTLIST struct_sheet_order range_id_1 CDATA #REQUIRED> <!ATTLIST struct_sheet_order range_id_2 CDATA #REQUIRED> <!ELEMENT sense (#PCDATA)> <!ELEMENT struct_sheet_range (sheet_range_begin_acid_id*, sheet_range_begin_asym_id*, sheet_range_begin_seq_id*, sheet_range_end_acid_id*, sheet_range_end_asym_id*, sheet_range_end_seq_id*)> <!ATTLIST struct_sheet_range struct_sheet_id CDATA #IMPLIED> <!ATTLIST struct_sheet_range range_id_1 CDATA #REQUIRED> <!ELEMENT sheet_range_begin_acid_id (#PCDATA)> <!ELEMENT sheet_range_begin_asym_id (#PCDATA)> <!ELEMENT sheet_range_begin_seq_id (#PCDATA)> <!ELEMENT sheet_range_end_acid_id (#PCDATA)> <!ELEMENT sheet_range_end_asym_id (#PCDATA)> <!ELEMENT sheet_range_end_seq_id (#PCDATA)> <!ELEMENT struct_sheet_hbond (range_1_atom_id*,range_1_acid_id*,range_1_asym_id*,range_1_seq_id*,range_2_atom_id*,range_2_acid_id*,range_2_asym_id*,range_2_seq_id* )> <!ATTLIST struct_sheet_hbond struct_sheet_id CDATA #IMPLIED> <!ATTLIST struct_sheet_hbond range_id_1 CDATA #REQUIRED> <!ATTLIST struct_sheet_hbond range_id_2 CDATA #REQUIRED> <!ELEMENT range_1_atom_id (#PCDATA)> <!ELEMENT range_1_acid_id (#PCDATA)> <!ELEMENT range_1_asym_id (#PCDATA)> <!ELEMENT range_1_seq_id (#PCDATA)> <!ELEMENT range_2_atom_id (#PCDATA)> <!ELEMENT range_2_acid_id (#PCDATA)> <!ELEMENT range_2_asym_id (#PCDATA)> <!ELEMENT range_2_seq_id (#PCDATA)> <!ELEMENT struct_turns (struct_turn*)> <!ATTLIST struct_turns pdb_id CDATA #IMPLIED> <!ELEMENT struct_turn (pdb_turn_id*, turn_begin_acid_id*, turn_begin_asym_id*, turn_begin_seq_id*,turn_begin_insertion_code*, turn_end_acid_id*, turn_end_asym_id*, turn_end_seq_id*,turn_end_insertion_code*, turn_details*)> <!ATTLIST struct_turn struct_turn_id CDATA #REQUIRED><!--order num--> <!ELEMENT pdb_turn_id (#PCDATA)> <!ELEMENT turn_begin_acid_id (#PCDATA)> <!ELEMENT turn_begin_asym_id (#PCDATA)> <!ELEMENT turn_begin_seq_id (#PCDATA)> <!ELEMENT turn_begin_insertion_code (#PCDATA)> <!ELEMENT turn_end_acid_id (#PCDATA)> <!ELEMENT turn_end_asym_id (#PCDATA)> <!ELEMENT turn_end_seq_id (#PCDATA)> <!ELEMENT turn_end_insertion_code (#PCDATA)> <!ELEMENT turn_details (#PCDATA)> <!ELEMENT bonds (bond*)> <!ATTLIST bonds pdb_id CDATA #IMPLIED> <!ELEMENT bond (bond_type*,part1_atom_name*,part1_location*,part1_chem_comp_id*,part1_auth_asym_id*,part1_seq_id*,part1_insertion_code*,hydro_atom_name*, hydro_location*,hydro_auth_asym_id*,hydro_seq_id*,hydro_insertion_code*,part2_atom_name*,part2_location*, part2_chem_comp_id*, part2_auth_asym_id*,part2_seq_id*,part2_insertion_code*,part1_symmetry*,part2_symmetry*)> <!ATTLIST bond bond_id CDATA #REQUIRED > <!ELEMENT bond_type (#PCDATA)><!--4 type #SS,H,Link,Salt--> <!ELEMENT part1_atom_name (#PCDATA)> <!ELEMENT part1_location (#PCDATA)> <!ELEMENT part1_chem_comp_id (#PCDATA)> <!ELEMENT part1_auth_asym_id (#PCDATA)> <!ELEMENT part1_seq_id (#PCDATA)><!--order num--> <!ELEMENT part1_insertion_code (#PCDATA)> <!ELEMENT hydro_atom_name (#PCDATA)> <!ELEMENT hydro_location (#PCDATA)> <!ELEMENT hydro_auth_asym_id (#PCDATA)> <!ELEMENT hydro_seq_id (#PCDATA)> <!ELEMENT hydro_insertion_code (#PCDATA)> <!ELEMENT part2_atom_name (#PCDATA)> <!ELEMENT part2_location (#PCDATA)> <!ELEMENT part2_chem_comp_id (#PCDATA)> <!ELEMENT part2_auth_asym_id (#PCDATA)> <!ELEMENT part2_seq_id (#PCDATA)> <!ELEMENT part2_insertion_code (#PCDATA)> <!ELEMENT part1_symmetry (#PCDATA)> <!ELEMENT part2_symmetry (#PCDATA)> <!ELEMENT protein_cis_es (protein_cis*)> <!ATTLIST protein_cis_es pdb_id CDATA #IMPLIED> <!ELEMENT protein_cis (cis_part1_chem_comp_id*, cis_part1_auth_asym_id*, cis_part1_seq_id*,cis_part2_chem_comp_id*, cis_part2_auth_asym_id*,cis_part2_seq_id*, cis_model_num*, cis_omega_angle*)> <!ATTLIST protein_cis protein_cis_id CDATA #REQUIRED > <!ELEMENT cis_part1_chem_comp_id (#PCDATA)> <!ELEMENT cis_part1_auth_asym_id (#PCDATA)> <!ELEMENT cis_part1_seq_id (#PCDATA)> <!ELEMENT cis_part2_chem_comp_id (#PCDATA)> <!ELEMENT cis_part2_auth_asym_id (#PCDATA)> <!ELEMENT cis_part2_seq_id (#PCDATA)> <!ELEMENT cis_model_num (#PCDATA)> <!ELEMENT cis_omega_angle (#PCDATA)> <!--****************************************************************--> <!-- The site element includes the content of SITE --> <!--****************************************************************--> <!ELEMENT sites (site*)> <!ATTLIST sites pdb_id CDATA #IMPLIED> <!ELEMENT site (site_name*, site_num_residues*, site_residues*)> <!ATTLIST site site_id CDATA #REQUIRED><!--#first column--> <!ELEMENT site_name (#PCDATA)> <!ELEMENT site_num_residues (#PCDATA)> <!ELEMENT site_residues (site_residue*)> <!ELEMENT site_residue (site_residue_name*, site_seq_type*, site_seq_id*, site_insertion_code*)> <!ATTLIST site_residue record_id CDATA #REQUIRED> <!ELEMENT site_residue_name (#PCDATA)> <!ELEMENT site_seq_type (#PCDATA)> <!ELEMENT site_seq_id (#PCDATA)> <!ELEMENT site_insertion_code (#PCDATA)> <!--****************************************************************--> <!--The crystal_cell element includes the content of CRYST1 --> <!--****************************************************************--> <!ELEMENT crystal_cell (length_a*,length_b*,length_c*,angle_alpha*,angle_beta*,angle_gamma*,space_group_name_H_M*,Z_pdb*)> <!ATTLIST crystal_cell pdb_id CDATA #IMPLIED> <!ELEMENT length_a (#PCDATA)> <!ELEMENT length_b (#PCDATA)> <!ELEMENT length_c (#PCDATA)> <!ELEMENT angle_alpha (#PCDATA)> <!ELEMENT angle_beta (#PCDATA)> <!ELEMENT angle_gamma (#PCDATA)> <!ELEMENT space_group_name_H_M (#PCDATA)> <!ELEMENT Z_pdb (#PCDATA)> <!--****************************************************************--> <!-- The orig_matrices element incudes the content of --> <!-- ORIGXn,SCALEn,MTRIXn,TVECT --> <!--****************************************************************--> <!ELEMENT orig_matrices (origmatrix*,transfer_matrix*,struct_ncs_oper_matrices*,translation_vectors*)> <!ATTLIST orig_matrices pdb_id CDATA #IMPLIED> <!ELEMENT origmatrix (origx11*, origx12*, origx13*, origx21*, origx22*, origx23*, origx31*, origx32*, origx33*, origx_vector1*, origx_vector2*, origx_vector3*)> <!ATTLIST origmatrix pdb_id CDATA #IMPLIED> <!ELEMENT origx11 (#PCDATA)> <!ELEMENT origx12 (#PCDATA)> <!ELEMENT origx13 (#PCDATA)> <!ELEMENT origx21 (#PCDATA)> <!ELEMENT origx22 (#PCDATA)> <!ELEMENT origx23 (#PCDATA)> <!ELEMENT origx31 (#PCDATA)> <!ELEMENT origx32 (#PCDATA)> <!ELEMENT origx33 (#PCDATA)> <!ELEMENT origx_vector1 (#PCDATA)> <!ELEMENT origx_vector2 (#PCDATA)> <!ELEMENT origx_vector3 (#PCDATA)> <!ELEMENT transfer_matrix (transfer_matrix11*, transfer_matrix12*, transfer_matrix13*, transfer_matrix21*, transfer_matrix22*, transfer_matrix23*, transfer_matrix31*, transfer_matrix32*, transfer_matrix33*, transfer_vector1*, transfer_vector2*, transfer_vector3*)> <!ATTLIST transfer_matrix pdb_id CDATA #IMPLIED> <!ELEMENT transfer_matrix11 (#PCDATA)> <!ELEMENT transfer_matrix12 (#PCDATA)> <!ELEMENT transfer_matrix13 (#PCDATA)> <!ELEMENT transfer_matrix21 (#PCDATA)> <!ELEMENT transfer_matrix22 (#PCDATA)> <!ELEMENT transfer_matrix23 (#PCDATA)> <!ELEMENT transfer_matrix31 (#PCDATA)> <!ELEMENT transfer_matrix32 (#PCDATA)> <!ELEMENT transfer_matrix33 (#PCDATA)> <!ELEMENT transfer_vector1 (#PCDATA)> <!ELEMENT transfer_vector2 (#PCDATA)> <!ELEMENT transfer_vector3 (#PCDATA)> <!ELEMENT struct_ncs_oper_matrices ( struct_ncs_oper_matrix* )> <!ELEMENT struct_ncs_oper_matrix (matrix11*, matrix12*, matrix13*, matrix21*, matrix22*, matrix23*, matrix31*, matrix32*, matrix33*, vector1*, vector2*, vector3*)> <!ATTLIST struct_ncs_oper_matrix oper_matrix_id CDATA #IMPLIED> <!ATTLIST struct_ncs_oper_matrix pdb_id CDATA #IMPLIED> <!ELEMENT matrix11 (#PCDATA)> <!ELEMENT matrix12 (#PCDATA)> <!ELEMENT matrix13 (#PCDATA)> <!ELEMENT matrix21 (#PCDATA)> <!ELEMENT matrix22 (#PCDATA)> <!ELEMENT matrix23 (#PCDATA)> <!ELEMENT matrix31 (#PCDATA)> <!ELEMENT matrix32 (#PCDATA)> <!ELEMENT matrix33 (#PCDATA)> <!ELEMENT vector1 (#PCDATA)> <!ELEMENT vector2 (#PCDATA)> <!ELEMENT vector3 (#PCDATA)> <!ELEMENT translation_vectors (translation_vector*)> <!ELEMENT translation_vector (translation_vector1*, translation_vector2*, translation_vector3*, translation_details*)> <!ATTLIST translation_vector t_vector_id CDATA #IMPLIED> <!ELEMENT translation_vector1 (#PCDATA)> <!ELEMENT translation_vector2 (#PCDATA)> <!ELEMENT translation_vector3 (#PCDATA)> <!ELEMENT translation_details (#PCDATA)> <!--*************************************************************--> <!--The model_atoms element includes the content of MODEL,ATOM, --> <!--SIGATM,ANISOU,SIGUIJ,TER,HETATM,ENDMDL --> <!--*************************************************************--> <!ELEMENT model_atoms (model_atom*)> <!ATTLIST model_atoms pdb_id CDATA #IMPLIED> <!ELEMENT model_atom (model*,atoms*)> <!ATTLIST model_atom model_atom_id CDATA #IMPLIED> <!ELEMENT model (model_serial_num*)> <!ATTLIST model model_id CDATA #REQUIRED> <!ELEMENT model_serial_num (#PCDATA)> <!ELEMENT atoms (atom*)> <!ATTLIST atoms pdb_id CDATA #IMPLIED> <!ELEMENT atom (atom_name*,atom_type*, atom_aminoacid_id*, atom_chem_comp_name*, atom_asym_id*, atom_location*, atom_entry_id*, atom_seq_id*, atom_num_neighbors*,atom_bonds*, atom_coordinator_x*, atom_coordinator_y*, atom_coordinator_z*, atom_occupancy*,b_iso_or_equiv*,sig_atom*,anisotropic_temp*,standard_devi_ansi*)> <!ATTLIST atom atom_site_id CDATA #REQUIRED> <!ATTLIST atom atom_classification CDATA #IMPLIED> <!ELEMENT atom_name (#PCDATA)> <!ELEMENT atom_type (#PCDATA)> <!ELEMENT atom_aminoacid_id (#PCDATA)> <!ELEMENT atom_chem_comp_name (#PCDATA)> <!ELEMENT atom_asym_id (#PCDATA)> <!ELEMENT atom_location EMPTY> <!ATTLIST atom_location loca_type (Begin|Middle|End) #REQUIRED> <!ELEMENT atom_entry_id (#PCDATA)> <!ELEMENT atom_seq_id (#PCDATA)> <!ELEMENT atom_num_neighbors (#PCDATA)> <!ELEMENT atom_bonds (atom_bond*)> <!ATTLIST atom_bonds num_bonds CDATA #IMPLIED> <!ELEMENT atom_bond (partner_atom_entry_id*, partner_atom_name*,atom_bond_type*)> <!ATTLIST atom_bond atom_bond_id CDATA #REQUIRED> <!ELEMENT partner_atom_entry_id (#PCDATA)> <!ELEMENT partner_atom_name (#PCDATA)> <!ELEMENT atom_bond_type (#PCDATA)> <!ELEMENT atom_coordinator_x (#PCDATA)> <!ELEMENT atom_coordinator_y (#PCDATA)> <!ELEMENT atom_coordinator_z (#PCDATA)> <!ELEMENT atom_occupancy (#PCDATA)> <!ELEMENT b_iso_or_equiv (#PCDATA)> <!ELEMENT sig_atom (standard_deviation_x*, standard_deviation_y*, standard_deviation_z*, standard_deviation_occupancy*)> <!ELEMENT standard_deviation_x (#PCDATA)> <!ELEMENT standard_deviation_y (#PCDATA)> <!ELEMENT standard_deviation_z (#PCDATA)> <!ELEMENT standard_deviation_occupancy (#PCDATA)> <!ELEMENT anisotropic_temp (anisotropic_temp_factor_11*, anisotropic_temp_factor_22*, anisotropic_temp_factor_33*, anisotropic_temp_factor_12*, anisotropic_temp_factor_13*, anisotropic_temp_factor_23)> <!ELEMENT anisotropic_temp_factor_11 (#PCDATA)> <!ELEMENT anisotropic_temp_factor_22 (#PCDATA)> <!ELEMENT anisotropic_temp_factor_33 (#PCDATA)> <!ELEMENT anisotropic_temp_factor_12 (#PCDATA)> <!ELEMENT anisotropic_temp_factor_13 (#PCDATA)> <!ELEMENT anisotropic_temp_factor_23 (#PCDATA)> <!ELEMENT standard_devi_ansi (standard_devi_ansi_11*, standard_devi_ansi_22*, standard_devi_ansi_33*, standard_devi_ansi_12*, standard_devi_ansi_13*, standard_devi_ansi_23)> <!ELEMENT standard_devi_ansi_11 (#PCDATA)> <!ELEMENT standard_devi_ansi_22 (#PCDATA)> <!ELEMENT standard_devi_ansi_33 (#PCDATA)> <!ELEMENT standard_devi_ansi_12 (#PCDATA)> <!ELEMENT standard_devi_ansi_13 (#PCDATA)> <!ELEMENT standard_devi_ansi_23 (#PCDATA)> <!--****************************************************************--> <!--The connections element includes the content of CONECT --> <!--****************************************************************--> <!ELEMENT connections (connection*)> <!ATTLIST connections pdb_id CDATA #IMPLIED> <!ELEMENT connection (auth_atom_serial_num*,partner_atoms*)> <!ATTLIST connection conn_id CDATA #REQUIRED> <!ELEMENT auth_atom_serial_num (#PCDATA)> <!ELEMENT partner_atoms (bonded_atoms*,hytrogen_atoms*,salt_atoms* )> <!ELEMENT bonded_atoms (bond_atom* )> <!ELEMENT bond_atom (bond_atom_serial_num* )> <!ATTLIST bond_atom bond_atom_id CDATA #REQUIRED> <!ELEMENT bond_atom_serial_num (#PCDATA)> <!ELEMENT hytrogen_atoms (h_atom* )> <!ELEMENT h_atom (h_atom_serial_num* )> <!ATTLIST h_atom h_atom_id CDATA #REQUIRED> <!ELEMENT h_atom_serial_num (#PCDATA)> <!ELEMENT salt_atoms (salt_atom* )> <!ELEMENT salt_atom (salt_atom_serial_num* )> <!ATTLIST salt_atom salt_atom_id CDATA #REQUIRED> <!ELEMENT salt_atom_serial_num (#PCDATA)> <!ELEMENT bookkeep_information (num_remarks?,num_seqs?,num_hets?,num_helixes?,num_sheets?,num_turns?,num_sites?,num_coords?,num_mods?,num_connections?)> <!ATTLIST bookkeep_information pdb_id CDATA #IMPLIED> <!ELEMENT num_remarks (#PCDATA)> <!ELEMENT num_seqs (#PCDATA)> <!ELEMENT num_hets (#PCDATA)> <!ELEMENT num_helixes (#PCDATA)> <!ELEMENT num_sheets (#PCDATA)> <!ELEMENT num_turns (#PCDATA)> <!ELEMENT num_sites (#PCDATA)> <!ELEMENT num_coords (#PCDATA)> <!ELEMENT num_mods (#PCDATA)> <!ELEMENT num_connections (#PCDATA)>