Atom Selection in the SilcsBio GUI

The SilcsBio GUI uses the same atom selection syntax as the NGL molecular structure viewer. This syntax is described at https://nglviewer.org/ngl/api/manual/selection-language.html and is reproduced below for convenience.

Keywords

  • 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)

Expressions

  • 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 number (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
10^A:F.CA%C/0

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

Atomindex

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

@0,1,4,5,11,23,42

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