Data items in the PDBX_VALIDATE_CHIRAL category list the residues that contain unexpected configuration of chiral centers. IMPROPER HA N C CB chirality CA IMPROPER HB1 HB2 CA CG stereo CB as this number approaches (+) or (-) 180.0, then the error in predicting the true chirality of the center increases. Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. HERE improper C---N----CA---CB done expected answer is around -120 mean -122.52 D-amino acid is +120.0 Example 1 <PDBx:pdbx_validate_chiralCategory> <PDBx:pdbx_validate_chiral id="1"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>0</PDBx:PDB_model_num> <PDBx:auth_asym_id>ASP</PDBx:auth_asym_id> <PDBx:auth_comp_id>B</PDBx:auth_comp_id> <PDBx:auth_seq_id>405</PDBx:auth_seq_id> <PDBx:details>ALPHA-CARBON</PDBx:details> <PDBx:omega>150.48</PDBx:omega> </PDBx:pdbx_validate_chiral> </PDBx:pdbx_validate_chiralCategory> |
<xsd:complexType name="pdbx_validate_chiralType"> <xsd:annotation> <xsd:documentation xml:lang="en">Data items in the PDBX_VALIDATE_CHIRAL category list the residues that contain unexpected configuration of chiral centers. IMPROPER HA N C CB chirality CA IMPROPER HB1 HB2 CA CG stereo CB as this number approaches (+) or (-) 180.0, then the error in predicting the true chirality of the center increases. Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. HERE improper C---N----CA---CB done expected answer is around -120 mean -122.52 D-amino acid is +120.0 Example 1 <PDBx:pdbx_validate_chiralCategory> <PDBx:pdbx_validate_chiral id="1"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>0</PDBx:PDB_model_num> <PDBx:auth_asym_id>ASP</PDBx:auth_asym_id> <PDBx:auth_comp_id>B</PDBx:auth_comp_id> <PDBx:auth_seq_id>405</PDBx:auth_seq_id> <PDBx:details>ALPHA-CARBON</PDBx:details> <PDBx:omega>150.48</PDBx:omega> </PDBx:pdbx_validate_chiral> </PDBx:pdbx_validate_chiralCategory></xsd:documentation> </xsd:annotation> <xsd:sequence> <xsd:element name="pdbx_validate_chiral" minOccurs="0" maxOccurs="unbounded"> <xsd:complexType> <xsd:all> <xsd:element name="PDB_ins_code" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string"> <xsd:annotation> <xsd:documentation xml:lang="en">Optional identifier of the residue This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category.</xsd:documentation> </xsd:annotation> </xsd:element> <xsd:element name="PDB_model_num" minOccurs="1" maxOccurs="1" type="xsd:integer"> <xsd:annotation> <xsd:documentation xml:lang="en">The model number for the given residue This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category.</xsd:documentation> </xsd:annotation> </xsd:element> <xsd:element name="auth_asym_id" minOccurs="1" maxOccurs="1" type="xsd:string"> <xsd:annotation> <xsd:documentation xml:lang="en">Part of the identifier of the residue This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category.</xsd:documentation> </xsd:annotation> </xsd:element> <xsd:element name="auth_atom_id" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string"> <xsd:annotation> <xsd:documentation xml:lang="en">Part of the identifier of the residue This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category.</xsd:documentation> </xsd:annotation> </xsd:element> <xsd:element name="auth_comp_id" minOccurs="1" maxOccurs="1" type="xsd:string"> <xsd:annotation> <xsd:documentation xml:lang="en">Part of the identifier of the residue This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category.</xsd:documentation> </xsd:annotation> </xsd:element> <xsd:element name="auth_seq_id" minOccurs="1" maxOccurs="1" type="xsd:string"> <xsd:annotation> <xsd:documentation xml:lang="en">Part of the identifier of the residue This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category.</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">A description of the outlier angle e.g. ALPHA-CARBON</xsd:documentation> </xsd:annotation> </xsd:element> <xsd:element name="label_alt_id" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string"> <xsd:annotation> <xsd:documentation xml:lang="en">Part of the identifier of the residue This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category.</xsd:documentation> </xsd:annotation> </xsd:element> <xsd:element name="omega" minOccurs="1" maxOccurs="1" nillable="true"> <xsd:annotation> <xsd:documentation xml:lang="en">The value of the OMEGA angle for the peptide linkage between the two defined residues</xsd:documentation> </xsd:annotation> <xsd:simpleType> <xsd:restriction base="xsd:decimal"> <xsd:minInclusive value="-180.0"/> <xsd:maxInclusive value="180.0"/> </xsd:restriction> </xsd:simpleType> </xsd:element> </xsd:all> <xsd:attribute name="id" use="required" type="xsd:integer"> <xsd:annotation> <xsd:documentation xml:lang="en">The value of attribute id in category pdbx_validate_chiral must uniquely identify each item in the PDBX_VALIDATE_CHIRAL list. This is an integer serial number.</xsd:documentation> </xsd:annotation> </xsd:attribute> </xsd:complexType> </xsd:element> </xsd:sequence> </xsd:complexType> |