Selection Syntax

• general format:

 [chain]:[residues].[atoms]

• an entire expression can be negated with !
• a chain/segment/atom/residue selection is negated with ^
• + corresponds to logical OR operator in specifying multiple residues/atoms
• / corresponds to logical AND operator
•  ? finds first occurence of amino acid sequence

• entirely different selections can be combined with _ (logical OR)

Examples:

• select chain(s):

 A:                     (chain A)
 A+B:                   (chain A or B)
 ^A:                    (not chain A)
 !A+B:                  (neither chain A nor B)

• select residue(s):

 PRO                    (proline) 
 GUA+ADE                (guanine or adenine)
 2-5                    (residues 2 through 5)
 hydrophobic            (hydrophobic residues)
 hetero/^HOH            (hetero groups except for HOH)

• select atoms(s):

 CA                     (Calpha)
 CA+CB                  (Calpha or Cbeta)

• combined residues/atoms:

 GUA.O1P                (O1P of guanine residues)
 ALA+GLY.CA             (Calpha of alanine or glycine)

• combined chain/residues/atoms:

 A:GUA.base             (nucleotide base atoms of guanines in chain A)
 A:GUA/10-12.base       (guanine base atoms within residues 10 to 12 from chain A)

• different sets

 A:GUA.base_B:CYT.base  (guanine base atoms from chain A plus cytosine base atoms from chain B)

• search for sequence

 @LKYTA                 (find part of structure that matches sequence) 
 @LK/^10-20.CA          (sequence LK except for residues 10 through 20, Calpha atoms only)

• complete list of supported residue selections:

 [residue number range]
 [residue name]
  peptide
  protein
  basic
  acidic
  charged
  hydrophobic
  polar
  nucleic
  purine
  pyrimidine
  water
  metal
  ion
  hetero

• complete list of supported atom selections:

 [atom name]
  backbone
  sidechain
  sugar
  base
  heavy
  hydrogen
  oxygen
  nitrogen
  carbon
  sulfur
  phosphorus