AtomSets

Predefined Atom Sets

Jmol recognizes and uses several keywords or tokens for several purposes: commands in the scripting language, colors, etc. Among them, there are keywords for predefined atom sets:

By element names:

carbon, oxygen, hydrogen, sulphur, etc.

On PDB format, Jmol will identify the element from columns 77-78 (element symbol, right-justified). If this is absent, then it will interpret the "aton name" field (columns 13-14).

Note: there is currently (June 2006, Jmol 10.2) a bug by which Jmol may read calcium as alpha carbon based on its ID, although identification by element name works properly.

Parts in proteins:

Backbone

Inclusion in this set is determined by atom id*, as follows:

• Peptide bond: N, H (bound to N), CA (alpha carbon), HA (bound to CA), C (carbonyl carbon), O or O1 (bound to C)
• In glycine, the two equivalent hydrogens are both in the backbone set: either H1 and 1HA or 1HA and 2HA.

• Termini:
  • OXT : second carbonyl oxygen on C-terminus
  • 1H, 2H, 3H : terminal amino hydrogens

(*)Note: on PDB format: atom id is called atom name, and must be in these positions/columns:

• 13-14 : Chemical symbol, right justified, except for hydrogen atoms
• 15 : Remoteness indicator (alphabetic); e.g., in amino acid residues, alpha = A, beta = B, gamma = G, delta = D, epsilon = E.
• 16 : Branch designator (numeric).

Sidechain

Defined as (not backbone).

Parts in nucleic acids:

Backbone

Inclusion in this set is determined by atom id*, as follows:

• Phosphate groups:
  • phosphorus: P
  • oxygens bound to phosphorus: O1P, O2P

• Atoms in pentose:
  • carbon ring: C1', C2', C3', C4', C5'
  • hydrogens attached to carbon ring: H1', 1H2', 2H2' (only DNA), H3', H4', 1H5' and 2H5'
  • hydroxyls: O2', O3', O4', O5', 2HO' (H on 2'-hydroxyl, only RNA) (the ring oxygen is denoted O4, not O1).

Note: PDB files label pentose atoms with asterisk instead of prime signs. How does Jmol cope with this? Not much of a trouble: given the asterisk is a wildcard, "select C3*" will get pentose carbons either labeled with prime or asterisk!.

• Termini:
  • 5'-terminus oxygen (no phosphate): O5T
  • 5'-terminus hydrogen (attached to O5T or O5'): H5T
  • 3'-terminus hydrogen (on 3'-hydroxyl): H3T

• Atoms in bases:
  • ring, both purines and pyrimidines: N1, C2, N3, C4, C5, C6
  • ring, purines: N7, C8, N9
  • ring, pyrimidines: O2
  • substituents on ring:
    • in cytosine: N4
    • in guanine: N2
    • in adenine: N6
    • in thymine: C5M
    • in guanine and hypoxanthine: O6
    • in thymine and uracil: O4
    • in thiouracil: S4

(*)Note: on PDB format, atom id is called atom name, and must be in these positions/columns:

• 13-14 : Chemical symbol, right justified, except for hydrogen atoms
• 15 : Remoteness indicator (alphabetic).
• 16 : Branch designator (numeric).

Sidechain

Defined as (not backbone).

Bases

Synonim of sidechain.

By type of molecule:

protein, nucleic, dna, rna, water, solvent, ligand...

By type of residue:

Inclusion in this sets is determined by residue id (only as far as it is written in the adequate field in the molecular coordinate file, usually PDB format).

Residue IDs:

• Nucleotides: A, G, C, T, U
• Amino acids: the 3-letter standard abbreviation

Residue sets:

• Nucleotides: purine, pyrimidine, at, cg
• Amino acids:
  • acyclic, cyclic, aliphatic, aromatic,
  • large, medium, small
  • polar, nonpolar, hydrophobic, neutral, charged, acidic, negative, basic, positive, ...
  • buried, surface
• hetero, ions, ligand, water, solvent

By structure of the polymer:

• amino, protein, nucleic
• helix, sheet, turn
• bonded

Contributors

AngelHerraez, NicolasVervelle, Pimpim, JimHu, Miguel