Atom Expression

In order to specify a group of atoms in a molecule, the following five expressions are available.

The standard boolean connectives 'and', 'or' and 'not', and brackets can be used to construct a complex expression. The boolean connectives may be abbreviated as '&', '|', and '|', respectively.

element name
Element names, such as carbon or nitrogen, can be used to select atoms.

set based on residue property
a) amino acids in protein molecule

b) nucleotides

c) others

comparison operators
Parts of a molecule can be selected using equality, inequality and ordering operators on their properties. Possible operators are =, ==, <>, !=, /=, <, <=, > and >=, and possible property names are as follows.

residue range
A group of atoms in a molecule can be selected by the residue ID. For example, command 'select 3' selects atoms whose residue ID is 3, and 'select 3-10' selects atoms whose residue ID is larger than or equal to 3 and smaller than or equal to 10.

within expression
A within expression selects atoms that exist within a specified distance from another set of atoms. For example, 'select within(3.0, backbone) selects atoms within a 3.0 Angstrom radius of any atom in a protein or nucleic acid backbone.

primitive expression
A xPSSS expression selects a group of atoms according to molecule's properties defined in the 'PDBML plus' file. It takes the following form; xps3:keyword. For example, 'select xps3:binding'. The keywords available for each molecule are obtained by the 'show xps3' command.