Difference between revisions of "AtomSets"
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== Parts in proteins: == | == Parts in proteins: == | ||
=== Backbone === | === Backbone === | ||
| − | Inclusion in this set is determined by atom id, as follows: | + | 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) | * Peptide bond: N, H (bound to N), CA (alpha carbon), HA (bound to CA), C (carbonyl carbon), O or O1 (bound to C) | ||
| Line 15: | Line 15: | ||
** OXT : second carbonyl oxygen on C-terminus | ** OXT : second carbonyl oxygen on C-terminus | ||
** 1H, 2H, 3H : terminal amino hydrogens | ** 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 === | === Sidechain === | ||
Revision as of 07:33, 6 June 2006
Contents
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)
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!.
- 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
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, ...
