Selection Language

Miew allows to view different molecule parts (subsets of atoms) using specific visualizations. To select these subsets one should use a Selection Language; its syntax is described below.

Quick Examples

  • chain A and not hetatm
    select all atoms in chain A except for HETATM PDB records.

  • residue ALA
    select all residues named ALA (alanine).

  • serial 1:10, 20:30 and type C, N
    select Carbon and Nitrogen atoms with atom indices in range 1 through 10 or 20 through 30 inclusively.

Syntax

An Expression in Miew selection language consists of a Selector or a set of Expressions joined with logical operations AND, OR, NOT and brackets for grouping.

Expression ::=
  Selector |
  Expression 'AND' Expression |
  Expression 'OR' Expression |
  'NOT' Expression |
  '(' Expression ')'

Selector consists of a keyword followed by an optional comma separated parameter list. Some keywords accept integer parameters (e.g. atom or residue indices), others accept strings (e.g. atom or residue names). Keywords are case insensitive.

Integer parameter can be a single value or range of values, where range borders are delimited by a colon. Example: 3:7 defines an integer range: 3, 4, 5, 6, and 7).

String parameters should be flanked by quotation marks unless the string consists of letters, digits and underscores only.

Selector ::=
  Keyword |
  Keyword IntegerList |
  Keyword StringList

IntegerList ::= Range | IntegerList ',' Range
Range ::= Number | Number ':' Number

StringList ::= String | StringList ',' String
String ::= AlphaNumericString | QuotedString

Keywords list

Keyword

Description

Example

all

all atoms

all

none

empty subset

none

hetatm

atoms defined as HETATM in PDB-file

not hetatm

water

water residues (WAT, HOH, H2O)

hetatm and not water

serial int

atoms by serial numbers

serial 1:10, 13, 25:37

name str

atoms by names

name CA, CB

elem str

atoms by chemical elements

elem O, N, H

polarh

polar hydrogens

polarh

nonpolarh

non-polar hydrogens

not nonpolarh

altloc str

atoms by alternative location (conformation)

altloc " ", A

residue str

residues by names

residue ALA, CYS

sequence int

residues by indices in a sequence

sequence 35:37

residx int

residues by ordinal index

residx 1327

icode str

residues by insertion code

sequence 409 and icode B

protein

one of 22 common amino acid residues

basic

basic amino acid residue: ARG, HIS, LYS

acidic

acidic amino acid residue: ASP, GLU

charged

basic or acidic residue

polar

polar amino acid residue: ASN, CYS, GLN, SER, THR, TYR

nonpolar

non-polar amino acid residue: ALA, ILE, LEU, MET, PHE, PRO, TRP, VAL

aromatic

aromatic amino acid residue: PHE, TRP, TYR

nucleic

nucleic residue

purine

purine nucleic residue: A, G, I and variations

pyrimidine

pyrimidine nucleic residue: C, T, U and variations

chain str

chain by name

chain A, C, E