PDBx:em_3d_fittingType

<xsd:complexType name="em_3d_fittingType">
  <xsd:annotation>
    <xsd:documentation xml:lang="en">Data items in the 3D_FITTING category record details of the method of fitting atomic coordinates from a PDB file into a 3d-em volume map file Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_3d_fittingCategory> <PDBx:em_3d_fitting entry_id="1DYL" id="1"> <PDBx:details> THE CRYSTAL STRUCTURE OF THE CAPSID PROTEIN FROM CHOI ET AL (1997) PROTEINS 3 27:345-359 (SUBUNIT A OF PDB FILE 1VCQ) WAS PLACED INTO THE CRYO-EM DENSITY MAP. THE CAPSID PROTEIN WAS FIRST MANUALLY POSITIONED INTO THE CRYO-EM DENSITY CORRESPONDING TO POSITIONS OF THE FOUR INDEPENDENT MONOMER DENSITIES BETWEEN THE INNER LEAFLET OF THE BILAYER AND THE RNA. THESE POSITIONS WERE THEN REFINED BY RIGID BODY REFINEMENT IN REAL SPACE WITH THE PROGRAM EMFIT (CHENG ET AL. 1995, CELL 80, 621-630). THE QUALITY OF THE FIT CAN BE SEEN FROM THE MAP DENSITY WITHIN THE PROTEIN. ALL 4563 ATOMS ARE IN DENSITY OF AT LEAST 4 SIGMA (96.73) ABOVE THE AVERAGE (512.04), 1167 ATOMS ARE IN DENSITY BETWEEN 4 AND 5 SIGMA, 3174 ATOMS ARE IN DENSITY BETWEEN 5 AND 6 SIGMA, AND 222 ATOMS ARE IN DENSTY OF 6 SIGMA OR ABOVE. THE VARIATION IN DENSITY OVER THE FITTED PROTEIN CAN BE VISUALIZED WITH THE PSEUDO TEMPERATURE FACTOR. THE DENSITY VALUE AT EACH ATOM IS GIVEN IN THE 8TH COLUM (USUALLY THE OCCUPANCY) AS THE NUMBER OF STANDARD DEVIATION ABOVE BACKGROUND. COLUMN NINE (USUALLY THE TEMPERATURE FACTOR) CONTAINS THE VALUE OF THE RELATIVE DENSITY WITHIN THE FITTED PROTEIN SCALED LINEARLY SO THAT THE MINIMUM DENSITY IS 100.0 AND THE MAXIMUM DENSITY IS 1.0. THE ATOMS THAT LIE IN THE LOWER DENSITY REGIONS WILL HAVE THE HIGHEST PSEUDO TEMPERATURE FACTORS.</PDBx:details> <PDBx:method>AUTOMATIC</PDBx:method> <PDBx:overall_b_value xsi:nil="true" /> <PDBx:ref_protocol>RIGID BODY REFINEMENT</PDBx:ref_protocol> <PDBx:ref_space>REAL</PDBx:ref_space> <PDBx:software_name>1</PDBx:software_name> <PDBx:target_criteria>R-FACTOR</PDBx:target_criteria> </PDBx:em_3d_fitting> </PDBx:em_3d_fittingCategory></xsd:documentation>
  </xsd:annotation>
  <xsd:sequence>
    <xsd:element name="em_3d_fitting" minOccurs="0" maxOccurs="unbounded">
      <xsd:complexType>
        <xsd:all>
          <xsd:element name="details" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">Any additional details regarding fitting of atomic coordinates into the 3d-em volume. Initial local fitting was done using Chimera and then NMFF was used for flexible fitting.</xsd:documentation>
            </xsd:annotation>
          </xsd:element>
          <xsd:element name="method" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">The method used to fit atomic coordinates into the 3dem reconstructed map. Local refinement, Flexible fitting</xsd:documentation>
            </xsd:annotation>
          </xsd:element>
          <xsd:element name="overall_b_value" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">The overall B (temperature factor) value for the 3d-em volume. 200</xsd:documentation>
            </xsd:annotation>
          </xsd:element>
          <xsd:element name="ref_protocol" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">The type of protocol used in the refinement. rigid body</xsd:documentation>
            </xsd:annotation>
          </xsd:element>
          <xsd:element name="ref_space" minOccurs="0" maxOccurs="1" nillable="true">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">A flag to indicate whether fitting was carried out in real or reciprocal refinement space. Real Reciprocal</xsd:documentation>
            </xsd:annotation>
            <xsd:simpleType>
              <xsd:restriction base="xsd:string">
                <xsd:enumeration value="REAL"/>
                <xsd:enumeration value="RECIPROCAL"/>
              </xsd:restriction>
            </xsd:simpleType>
          </xsd:element>
          <xsd:element name="software_name" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">The software used for fitting atomic coordinates to the map. Situs, NMFF, YUP.scx, etc.</xsd:documentation>
            </xsd:annotation>
          </xsd:element>
          <xsd:element name="target_criteria" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">The quality of fit of the atomic coordinates into the 3dem volume map. Cross-correlation coefficient</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 _entry_id in the ENTRY category.</xsd:documentation>
          </xsd:annotation>
        </xsd:attribute>
        <xsd:attribute name="id" use="required" type="xsd:string">
          <xsd:annotation>
            <xsd:documentation xml:lang="en">The value of attribute id in category em_3d_fitting must uniquely identify a fitting procedure of atomic coordinates into 3dem reconstructed volume map.</xsd:documentation>
          </xsd:annotation>
        </xsd:attribute>
      </xsd:complexType>
    </xsd:element>
  </xsd:sequence>
</xsd:complexType>