NGL@0.10.5-12 Home Manual Reference Source GalleryRepository
Manual » Usage

Selection Language

Selections (or 'Sele' for short) strings can be input at various places in the user interface or when scripting. They are used to limit which atoms/residues are shown in a [molecular representation]{@tutorial molecular-representations} or what atoms are loaded from a trajectory.


Select the side-chain and C-alpha atoms plus the backbone nitrogen in case of proline. not backbone or .CA or (PRO and .N) This selection is useful to display the sidechains together with a backbone trace. Hence there is also the keyword sidechainAttached for it.



  • all, *
  • sidechain
  • sidechainAttached (not backbone or .CA or (PRO and .N))
  • backbone
  • protein
  • nucleic
  • rna
  • dna
  • hetero
  • ligand (( not polymer or hetero ) and not ( water or ion ))
  • ion
  • saccharide/sugar
  • polymer
  • water
  • hydrogen
  • helix
  • sheet
  • turn (not helix and not sheet)
  • small (Gly or Ala or Ser)
  • nucleophilic (Ser or Thr or Cys)
  • hydrophobic (Ala or Val or Leu or Ile or Met or Pro or Phe or Trp)
  • aromatic (Phe or Tyr or Trp or His)
  • amid (Asn or Gln)
  • acidic (Asp or Glu)
  • basic (His or Lys or Arg)
  • charged (Asp or Glu or His or Lys or Arg)
  • polar (Asp or Cys or Gly or Glu or His or Lys or Arg or Asn or Gln or Ser or Thr or Tyr)
  • nonpolar (Ala or Ile or Leu or Met or Phe or Pro or Val or Trp)
  • cyclic (His or Phe or Pro or Trp or Tyr)
  • aliphatic (Ala or Gly or Ile or Leu or Val)
  • bonded (all atoms with at least one bond)
  • ring (all atoms within rings)


  • residue number: 1, 2, 100
  • residue number range: 3-40 (Note that around the dash - no spaces are allowed)
  • chain name: :A
  • atom name: .CA, .C, .N, ...
  • model: /0, /1, ...
  • residue name: ALA, GLU, SOL, DMPC, ...
  • numeric residue name: [032], [1AB], ...
  • list of residue names: [ALA,GLU,MET], [ARG,LYS], ...
  • element name: _H, _C, _O, ...
  • alternate location: %A, %B, ... or % for non-alternate location atoms
  • insertion code: ^A, ^B, ... or ^ for residues with no insertion code

Some of these expressions can be combined (in this order) - residue numer (range), insertion code, chain name, atom name, alternate location, model - like this

// select C-alpha atoms of residue 10 with insertion code A
// from chain F in model 0 at alternate location C

which is the same as

10 and ^A and :F and .CA and %C and /0

Single expressions may be left out as long as the order (see above) is kept, for example:

:A/0 # select chain A from model 0


A list of atom indices can be given as a comma seperated list (no spaces in between) prefixed with the @ character.


Logical operators (in order of binding strength)

  • NOT
  • AND
  • OR

Additionally, parentheses () can be used for grouping: :A and ( 1 or 10 or 100 ) # select residues 1, 10 and 100 from chain A