Difference between revisions of "AtomSets"

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(Backbone)
(Backbone)
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== Parts in nucleic acids: ==
 
== Parts in nucleic acids: ==
 
=== Backbone ===
 
=== Backbone ===
Inclusion in this set is determined by atom id, as follows:
+
Inclusion in this set is determined by atom id*, as follows:
  
 
* Phosphate groups:
 
* Phosphate groups:
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** carbon ring: C1', C2', C3', C4', C5'
 
** carbon ring: C1', C2', C3', C4', C5'
 
** hydrogens attached to carbon ring: H1', 1H2', 2H2' (only DNA), H3', H4', 1H5' and 2H5'
 
** 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)
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** hydroxyls: O2', O3', O4', O5', 2HO' (H on 2'-hydroxyl, only RNA) (the ring oxygen is denoted O4, not O1).
  
<blockquote>Note: some (many?) 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!.
+
<blockquote>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!.
 
</blockquote>
 
</blockquote>
  
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*** O4 in T and U
 
*** O4 in T and U
 
*** S4 unique to thio-U
 
*** S4 unique to thio-U
 +
 +
(*)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 ===
 
=== Sidechain ===

Revision as of 07:39, 6 June 2006

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.

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 glicine, the two equivalent H 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

(*) 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:
    • O5T : 5'-terminus oxygen (no phosphate)
    • H5T : 5'-terminus hydrogen (attached to O5T or O5')
    • H3T : 3'-terminus hydrogen (on 3'-hydroxyl)
  • 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:
      • N4 unique to C
      • N2 unique to G
      • N6 unique to A
      • C5M unique to T
      • O6 in G and I
      • O4 in T and U
      • S4 unique to thio-U

(*)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
  • Amino acids: polar, nonpolar, charged, acidic, negative, basic, positive, aromatic, ...