PDBML-extatom

PDBML-extatom files contain atomic coordinates in a "simplified" format. The XML schema for PDBML-extatom format is provided at:

• https://pdbj.org//schema/pdbx-v40-ext.xsd

And can also be viewed using our interactive XML viewer.

In the canonical PDBML files, the atomic coordinates and related information are given in the atom_site elements. For example,

   <PDBx:atom_siteCategory>
      <PDBx:atom_site id="1">
         <PDBx:B_iso_or_equiv>53.29</PDBx:B_iso_or_equiv>
         <PDBx:B_iso_or_equiv_esd xsi:nil="true" />
         <PDBx:Cartn_x>101.601</PDBx:Cartn_x>
         <PDBx:Cartn_x_esd xsi:nil="true" />
         <PDBx:Cartn_y>38.534</PDBx:Cartn_y>
         <PDBx:Cartn_y_esd xsi:nil="true" />
         <PDBx:Cartn_z>-1.962</PDBx:Cartn_z>
         <PDBx:Cartn_z_esd xsi:nil="true" />
         <PDBx:auth_asym_id>A</PDBx:auth_asym_id>
         <PDBx:auth_atom_id>N</PDBx:auth_atom_id>
         <PDBx:auth_comp_id>VAL</PDBx:auth_comp_id>
         <PDBx:auth_seq_id>1</PDBx:auth_seq_id>
         <PDBx:group_PDB>ATOM</PDBx:group_PDB>
         <PDBx:label_alt_id></PDBx:label_alt_id>
         <PDBx:label_asym_id>A</PDBx:label_asym_id>
         <PDBx:label_atom_id>N</PDBx:label_atom_id>
         <PDBx:label_comp_id>VAL</PDBx:label_comp_id>
         <PDBx:label_entity_id>1</PDBx:label_entity_id>
         <PDBx:label_seq_id>1</PDBx:label_seq_id>
         <PDBx:occupancy>1.00</PDBx:occupancy>
         <PDBx:occupancy_esd xsi:nil="true" />
         <PDBx:pdbx_PDB_ins_code xsi:nil="true" />
         <PDBx:pdbx_PDB_model_num>1</PDBx:pdbx_PDB_model_num>
         <PDBx:pdbx_formal_charge xsi:nil="true" />
         <PDBx:type_symbol>N</PDBx:type_symbol>
      </PDBx:atom_site>
      <PDBx:atom_site id="2">
         <PDBx:B_iso_or_equiv>47.99</PDBx:B_iso_or_equiv>
         <PDBx:B_iso_or_equiv_esd xsi:nil="true" />
         <PDBx:Cartn_x>103.062</PDBx:Cartn_x>
         <PDBx:Cartn_x_esd xsi:nil="true" />
         <PDBx:Cartn_y>38.513</PDBx:Cartn_y>
         <PDBx:Cartn_y_esd xsi:nil="true" />
         <PDBx:Cartn_z>-2.159</PDBx:Cartn_z>
         <PDBx:Cartn_z_esd xsi:nil="true" />
         <PDBx:auth_asym_id>A</PDBx:auth_asym_id>
         <PDBx:auth_atom_id>CA</PDBx:auth_atom_id>
         <PDBx:auth_comp_id>VAL</PDBx:auth_comp_id>
         <PDBx:auth_seq_id>1</PDBx:auth_seq_id>
         <PDBx:group_PDB>ATOM</PDBx:group_PDB>
         <PDBx:label_alt_id></PDBx:label_alt_id>
         <PDBx:label_asym_id>A</PDBx:label_asym_id>
         <PDBx:label_atom_id>CA</PDBx:label_atom_id>
         <PDBx:label_comp_id>VAL</PDBx:label_comp_id>
         <PDBx:label_entity_id>1</PDBx:label_entity_id>
         <PDBx:label_seq_id>1</PDBx:label_seq_id>
         <PDBx:occupancy>1.00</PDBx:occupancy>
         <PDBx:occupancy_esd xsi:nil="true" />
         <PDBx:pdbx_PDB_ins_code xsi:nil="true" />
         <PDBx:pdbx_PDB_model_num>1</PDBx:pdbx_PDB_model_num>
         <PDBx:pdbx_formal_charge xsi:nil="true" />
         <PDBx:type_symbol>C</PDBx:type_symbol>
      </PDBx:atom_site>
...

The same information in the PDBML-extatom format is given as

    <PDBx:category_atom_record>
      <PDBx:atom_record id=      "1">  ATOM    1   A    A      1      1  ?  .  VAL  VAL   N  N  N   101.601    38.534    -1.962    1
.00   53.29     1    ? </PDBx:atom_record>
      <PDBx:atom_record id=      "2">  ATOM    1   A    A      1      1  ?  .  VAL  VAL   C  CA  CA   103.062    38.513    -2.159
 1.00   47.99     1    ? </PDBx:atom_record>...

Please refer to the PDBML-extatom XML schema for the meaning of each column.

See also:

• PDBML
• PDBML-noatom