PDBx:atom_sites

Element Information

Model

Attributes

QName Type Fixed Default Use Inheritable Annotation
entry_id xsd:string required
This data item is a pointer to attribute id in category entry in the ENTRY category.

Source

<xsd:element name="atom_sites" minOccurs="0" maxOccurs="unbounded">
  <xsd:complexType>
    <xsd:all>
      <xsd:element name="Cartn_transf_matrix11" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
        <xsd:annotation>
          <xsd:documentation xml:lang="en">The [1][1] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|</xsd:documentation>
        </xsd:annotation>
      </xsd:element>
      <xsd:element name="Cartn_transf_matrix12" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
        <xsd:annotation>
          <xsd:documentation xml:lang="en">The [1][2] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|</xsd:documentation>
        </xsd:annotation>
      </xsd:element>
      <xsd:element name="Cartn_transf_matrix13" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
        <xsd:annotation>
          <xsd:documentation xml:lang="en">The [1][3] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|</xsd:documentation>
        </xsd:annotation>
      </xsd:element>
      <xsd:element name="Cartn_transf_matrix21" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
        <xsd:annotation>
          <xsd:documentation xml:lang="en">The [2][1] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|</xsd:documentation>
        </xsd:annotation>
      </xsd:element>
      <xsd:element name="Cartn_transf_matrix22" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
        <xsd:annotation>
          <xsd:documentation xml:lang="en">The [2][2] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|</xsd:documentation>
        </xsd:annotation>
      </xsd:element>
      <xsd:element name="Cartn_transf_matrix23" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
        <xsd:annotation>
          <xsd:documentation xml:lang="en">The [2][3] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|</xsd:documentation>
        </xsd:annotation>
      </xsd:element>
      <xsd:element name="Cartn_transf_matrix31" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
        <xsd:annotation>
          <xsd:documentation xml:lang="en">The [3][1] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|</xsd:documentation>
        </xsd:annotation>
      </xsd:element>
      <xsd:element name="Cartn_transf_matrix32" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
        <xsd:annotation>
          <xsd:documentation xml:lang="en">The [3][2] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|</xsd:documentation>
        </xsd:annotation>
      </xsd:element>
      <xsd:element name="Cartn_transf_matrix33" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
        <xsd:annotation>
          <xsd:documentation xml:lang="en">The [3][3] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|</xsd:documentation>
        </xsd:annotation>
      </xsd:element>
      <xsd:element name="Cartn_transf_vector1" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
        <xsd:annotation>
          <xsd:documentation xml:lang="en">The [1] element of the three-element vector used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The rotation matrix is defined in attribute Cartn_transf_matrix[][]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|</xsd:documentation>
        </xsd:annotation>
      </xsd:element>
      <xsd:element name="Cartn_transf_vector2" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
        <xsd:annotation>
          <xsd:documentation xml:lang="en">The [2] element of the three-element vector used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The rotation matrix is defined in attribute Cartn_transf_matrix[][]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|</xsd:documentation>
        </xsd:annotation>
      </xsd:element>
      <xsd:element name="Cartn_transf_vector3" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
        <xsd:annotation>
          <xsd:documentation xml:lang="en">The [3] element of the three-element vector used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The rotation matrix is defined in attribute Cartn_transf_matrix[][]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|</xsd:documentation>
        </xsd:annotation>
      </xsd:element>
      <xsd:element name="Cartn_transform_axes" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
        <xsd:annotation>
          <xsd:documentation xml:lang="en">A description of the relative alignment of the crystal cell axes to the Cartesian orthogonal axes as applied in the transformation matrix attribute Cartn_transf_matrix[][] in category atom_sites. a parallel to x; b in the plane of y and z</xsd:documentation>
        </xsd:annotation>
      </xsd:element>
      <xsd:element name="fract_transf_matrix11" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
        <xsd:annotation>
          <xsd:documentation xml:lang="en">The [1][1] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|</xsd:documentation>
        </xsd:annotation>
      </xsd:element>
      <xsd:element name="fract_transf_matrix12" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
        <xsd:annotation>
          <xsd:documentation xml:lang="en">The [1][2] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|</xsd:documentation>
        </xsd:annotation>
      </xsd:element>
      <xsd:element name="fract_transf_matrix13" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
        <xsd:annotation>
          <xsd:documentation xml:lang="en">The [1][3] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|</xsd:documentation>
        </xsd:annotation>
      </xsd:element>
      <xsd:element name="fract_transf_matrix21" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
        <xsd:annotation>
          <xsd:documentation xml:lang="en">The [2][1] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|</xsd:documentation>
        </xsd:annotation>
      </xsd:element>
      <xsd:element name="fract_transf_matrix22" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
        <xsd:annotation>
          <xsd:documentation xml:lang="en">The [2][2] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|</xsd:documentation>
        </xsd:annotation>
      </xsd:element>
      <xsd:element name="fract_transf_matrix23" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
        <xsd:annotation>
          <xsd:documentation xml:lang="en">The [2][3] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|</xsd:documentation>
        </xsd:annotation>
      </xsd:element>
      <xsd:element name="fract_transf_matrix31" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
        <xsd:annotation>
          <xsd:documentation xml:lang="en">The [3][1] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|</xsd:documentation>
        </xsd:annotation>
      </xsd:element>
      <xsd:element name="fract_transf_matrix32" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
        <xsd:annotation>
          <xsd:documentation xml:lang="en">The [3][2] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|</xsd:documentation>
        </xsd:annotation>
      </xsd:element>
      <xsd:element name="fract_transf_matrix33" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
        <xsd:annotation>
          <xsd:documentation xml:lang="en">The [3][3] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|</xsd:documentation>
        </xsd:annotation>
      </xsd:element>
      <xsd:element name="fract_transf_vector1" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
        <xsd:annotation>
          <xsd:documentation xml:lang="en">The [1] element of the three-element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x3 rotation is defined in attribute fract_transf_matrix[][]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|</xsd:documentation>
        </xsd:annotation>
      </xsd:element>
      <xsd:element name="fract_transf_vector2" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
        <xsd:annotation>
          <xsd:documentation xml:lang="en">The [2] element of the three-element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x3 rotation is defined in attribute fract_transf_matrix[][]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|</xsd:documentation>
        </xsd:annotation>
      </xsd:element>
      <xsd:element name="fract_transf_vector3" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
        <xsd:annotation>
          <xsd:documentation xml:lang="en">The [3] element of the three-element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x3 rotation is defined in attribute fract_transf_matrix[][]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|</xsd:documentation>
        </xsd:annotation>
      </xsd:element>
      <xsd:element name="solution_hydrogens" minOccurs="0" maxOccurs="1" nillable="true">
        <xsd:annotation>
          <xsd:documentation xml:lang="en">This code identifies the method used to locate the hydrogen atoms. *** This data item would not in general be used in a macromolecular data block. ***</xsd:documentation>
        </xsd:annotation>
        <xsd:simpleType>
          <xsd:restriction base="xsd:string">
            <xsd:enumeration value="difmap"/>
            <xsd:enumeration value="vecmap"/>
            <xsd:enumeration value="heavy"/>
            <xsd:enumeration value="direct"/>
            <xsd:enumeration value="geom"/>
            <xsd:enumeration value="disper"/>
            <xsd:enumeration value="isomor"/>
          </xsd:restriction>
        </xsd:simpleType>
      </xsd:element>
      <xsd:element name="solution_primary" minOccurs="0" maxOccurs="1" nillable="true">
        <xsd:annotation>
          <xsd:documentation xml:lang="en">This code identifies the method used to locate the initial atom sites. *** This data item would not in general be used in a macromolecular data block. ***</xsd:documentation>
        </xsd:annotation>
        <xsd:simpleType>
          <xsd:restriction base="xsd:string">
            <xsd:enumeration value="difmap"/>
            <xsd:enumeration value="vecmap"/>
            <xsd:enumeration value="heavy"/>
            <xsd:enumeration value="direct"/>
            <xsd:enumeration value="geom"/>
            <xsd:enumeration value="disper"/>
            <xsd:enumeration value="isomor"/>
          </xsd:restriction>
        </xsd:simpleType>
      </xsd:element>
      <xsd:element name="solution_secondary" minOccurs="0" maxOccurs="1" nillable="true">
        <xsd:annotation>
          <xsd:documentation xml:lang="en">This code identifies the method used to locate the non-hydrogen-atom sites not found by attribute solution_primary. in category atom_sites *** This data item would not in general be used in a macromolecular data block. ***</xsd:documentation>
        </xsd:annotation>
        <xsd:simpleType>
          <xsd:restriction base="xsd:string">
            <xsd:enumeration value="difmap"/>
            <xsd:enumeration value="vecmap"/>
            <xsd:enumeration value="heavy"/>
            <xsd:enumeration value="direct"/>
            <xsd:enumeration value="geom"/>
            <xsd:enumeration value="disper"/>
            <xsd:enumeration value="isomor"/>
          </xsd:restriction>
        </xsd:simpleType>
      </xsd:element>
      <xsd:element name="special_details" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
        <xsd:annotation>
          <xsd:documentation xml:lang="en">Additional information about the atomic coordinates not coded elsewhere in the CIF.</xsd:documentation>
        </xsd:annotation>
      </xsd:element>
    </xsd:all>
    <xsd:attribute name="entry_id" use="required" type="xsd:string">
      <xsd:annotation>
        <xsd:documentation xml:lang="en">This data item is a pointer to attribute id in category entry in the ENTRY category.</xsd:documentation>
      </xsd:annotation>
    </xsd:attribute>
  </xsd:complexType>
</xsd:element>

Sample