<xsd:complexType name="em_3d_reconstructionType">
<xsd:annotation>
<xsd:documentation xml:lang="en">Data items in the EM_3D_RECONSTRUCTION category record details of the 3D reconstruction procedure from 2D projections. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_3d_reconstructionCategory> <PDBx:em_3d_reconstruction entry_id="1DYL" id="1"> <PDBx:actual_pixel_size>2.52</PDBx:actual_pixel_size> <PDBx:citation_id>1</PDBx:citation_id> <PDBx:ctf_correction_method xsi:nil="true" /> <PDBx:details xsi:nil="true" /> <PDBx:method>CROSS-COMMON LINES</PDBx:method> <PDBx:nominal_pixel_size>2.64</PDBx:nominal_pixel_size> <PDBx:resolution>9</PDBx:resolution> <PDBx:resolution_method xsi:nil="true" /> </PDBx:em_3d_reconstruction> </PDBx:em_3d_reconstructionCategory></xsd:documentation>
</xsd:annotation>
<xsd:sequence>
<xsd:element name="em_3d_reconstruction" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:all>
<xsd:element name="actual_pixel_size" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
<xsd:annotation>
<xsd:documentation xml:lang="en">The actual pixel size of projection set of images. 2.8 5.76</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="citation_id" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
<xsd:annotation>
<xsd:documentation xml:lang="en">This data item is a pointer to attribute id in category citation in the CITATION category.</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="ctf_correction_method" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
<xsd:annotation>
<xsd:documentation xml:lang="en">The CTF-correction method. The Contrast Transfer Function CTF compensation for low contrast specimens (e.g. frozen-hydrated), for which phase contrast is the only significant mechanism, then higher defocus levels must be used to achieve any significant transfer, and several images at different focus levels must be combined to complete the information lost from the transfer gaps of any one image. The CTF correction can be applied to each extracted particle separately or to the whole micrograph after digitisation. The simplest level of compensation is to reverse phases at the negative lobes of the CTF. The volumes were CTF-corrected in defocus groups, with an average of approximately 999 individual images per group</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="details" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
<xsd:annotation>
<xsd:documentation xml:lang="en">Any additional details used in the 3d reconstruction. a modified version of SPIDER program was used for the reconstruction</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="euler_angles_details" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
<xsd:annotation>
<xsd:documentation xml:lang="en">euler angles details</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="magnification_calibration" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
<xsd:annotation>
<xsd:documentation xml:lang="en">The magnification calibration method for the 3d reconstruction. TMV images</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 algorithm method used for the 3d-reconstruction. cross-common lines polar Fourier transform (PFT)</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="nominal_pixel_size" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
<xsd:annotation>
<xsd:documentation xml:lang="en">The nominal pixel size of the projection set of images. 3.11 6.78</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="num_class_averages" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:integer">
<xsd:annotation>
<xsd:documentation xml:lang="en">This item was correspondence to two type of em dataset processing_emDataSet_singleParticle.numClassAverages processing_emDataSet_icosahedral.numClassAverages</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="num_particles" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:integer">
<xsd:annotation>
<xsd:documentation xml:lang="en">The number of particles used in the 3d reconstruction</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="resolution" minOccurs="0" maxOccurs="1" nillable="true">
<xsd:annotation>
<xsd:documentation xml:lang="en">The final resolution (in angstroms)of the 3d reconstruction. 8.9 10.0</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:simpleContent>
<xsd:extension base="xsd:decimal">
<xsd:attribute fixed="angstroms" name="units" type="xsd:string" use="optional"/>
</xsd:extension>
</xsd:simpleContent>
</xsd:complexType>
</xsd:element>
<xsd:element name="resolution_method" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
<xsd:annotation>
<xsd:documentation xml:lang="en">The method used to determine the final resolution of the 3d reconstruction. The Fourier Shell Correlation criterion as a measure of resolution is based on the concept of splitting the (2D) data set into two halves; averaging each and comparing them using the Fourier Ring Correlation (FRC) technique. FSC at 0.5 cut-off</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="software" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
<xsd:annotation>
<xsd:documentation xml:lang="en">software name</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:attribute name="id" use="required" type="xsd:string">
<xsd:annotation>
<xsd:documentation xml:lang="en">The value of attribute id in category em_3d_reconstruction must uniquely identify the 3d reconstruction.</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
</xsd:complexType> |