Difference between revisions of "AtomSets"
AngelHerraez (talk | contribs) (→Backbone) |
AngelHerraez (talk | contribs) (→Backbone) |
||
Line 26: | Line 26: | ||
== 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: | ||
Line 35: | Line 35: | ||
** 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) | + | ** hydroxyls: O2', O3', O4', O5', 2HO' (H on 2'-hydroxyl, only RNA) (the ring oxygen is denoted O4, not O1). |
− | <blockquote>Note: | + | <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> | ||
Line 57: | Line 57: | ||
*** 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
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) (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, ...