Atom Expression

From jV

Contents 1 predefined set 1.1 element name 1.2 set based on residue property 1.3 others 2 comparison operators 3 residue range 4 within expression 5 PDBj expression 6 primitive expression

In order to specify a group of atoms in a molecule, the following five expressions are available.

The standard boolean connectives 'and', 'or' and 'not', and brackets can be used to construct a complex expression. The boolean connectives may be abbreviated as '&', '|', and '!', respectively.

predefined set

element name

Element names, such as carbon or nitrogen, can be used to select atoms.

set based on residue property

a) amino acids in protein molecule

ALA

ARG

ASN

ASP

CYS

GLU

GLN

GLY

HIS

ILE

LEU

LYS

MET

PHE

PRO

SER

THR

TRP

TYR

VAL

Acidic

*

*

Acyclic

*

*

*

*

*

*

*

*

*

*

*

*

*

*

*

Aliphatic

*

*

*

*

*

Aromatic

*

*

*

*

Basic

*

*

*

Buried

*

*

*

*

*

*

*

*

Charged

*

*

*

*

*

Cyclic

*

*

*

*

*

Hydrophobic

*

*

*

*

*

*

*

*

*

*

Large

*

*

*

*

*

*

*

*

*

*

*

Medium

*

*

*

*

*

*

Negative

*

*

Neutral

*

*

*

*

*

*

*

*

*

*

*

*

*

*

*

*

Polar

*

*

*

*

*

*

*

*

*

*

Positive

*

*

*

Small

*

*

Surface

*

*

*

*

*

*

*

*

*

*

*

*

Cysteine

*

Amino

above 20 amino acids + other amino acids

Protein

above 'Amino' set + UNK, ACE + FOR (PDB version 2.3 only)

Here, 'other amino acids' stands for components whose type is one of the followings in Chemical Component Dictionary.
D-PEPTIDE LINKING
D-PEPTIDE NH3 AMINO TERMINUS
L-PEPTIDE COOH CARBOXY TERMINUS
L-PEPTIDE LINKING
L-PEPTIDE NH3 AMINO TERMINUS
PEPTIDE LINKING
PEPTIDE-LIKE

b1) nucleotides (for PDB version 2.3)

A

C

G

T

U

+U

I

1MA

5MC

OMC

1MG

2MG

M2G

7MG

OMG

YG

H2U

5MU

PSU

AT

*

*

CG

*

*

Purine

*

*

Pyrimidine

*

*

DNA

*

*

*

*

RNA

*

*

*

*

*

*

*

*

*

*

*

*

*

*

*

*

*

*

Nucleic

*

*

*

*

*

*

*

*

*

*

*

*

*

*

*

*

*

*

*

b2) nucleotides (for PDB version 3)

	DA	DC	DG	DT	A	C	G	U	other DNA	other RNA
AT	*			*
CG		*	*
Purine	*		*		*		*
Pyrimidine		*		*		*		*
DNA	*	*	*	*					*
RNA					*	*	*	*		*
Nucleic	*	*	*	*	*	*	*	*	*	*

Here, 'other DNA' and 'other RNA' stand for components whose type is DNA LINKING and RNA LINKING respectively in Chemical Component Dictionary.

c) others

	HOH	DOD	SO4	PO4
Water	*	*
Ions			*	*
Solvent	*	*	*	*

others

Alpha	atoms whose name is CA.
Hetero	atoms written as HETATM in PDB files or atoms in Solvent set.
Ligand	atoms in Hetero set and not in Solvent set.
Backbone Mainchain	atoms in Amino set whose name is N, CA, C or O, or atoms in Nuceic set whose name is P,O1P,O2P,O5*,C5*,C4*,O4*,C3*,O3*,C2*,O2* or C1*.
Sidechain	atoms in Amino set or Nucleic set and not in Backbone set.
Bonded	atoms that is connected to at least one other atom.
Selected	atoms currently selected.
Helix	atoms in the alpha-helix structure.
Sheet	atoms in the beta-sheet structure.
Turn	atoms in the turn structure.

comparison operators

Parts of a molecule can be selected using equality, inequality and ordering operators on their properties. Possible operators are =, ==, <>, !=, /=, <, <=, > and >=, and possible property names are as follows.

AtomNo	atom ID in PDB files.
ElemNo	atomic number.
ResNo	residue ID in PDB files.
Radius	radius of a ball image of atoms.
Temperature	temperature factor of atoms.
Model	model ID in PDB files.
File	File ID.

residue range

A group of atoms in a molecule can be selected by the residue ID. For example, command 'select 3' selects atoms whose residue ID is 3, and 'select 3-10' selects atoms whose residue ID is larger than or equal to 3 and smaller than or equal to 10. Optionally, the chain ID can be specified after residue range with a colon. For example, command 'select 3:A' selects atoms whose residue ID is 3 in the A chain. The chain ID can be specified in several ways (see primitive expression).

within expression

A within expression selects atoms that exist within a specified distance from another set of atoms. For example, 'select within(3.0, backbone) selects atoms within a 3.0 Angstrom radius of any atom in a protein or nucleic acid backbone.

PDBj expression

A PDBj expression selects a group of atoms according to molecule's properties defined in the PDBMLplus file. It takes the following form;

pdbj:keyword

For example, 'select pdbj:binding'. The keywords available for each molecule are obtained by the 'show pdbj' command.

primitive expression

A primitive expression takes such a form as

residue name[residue ID][:chain ID][.atom name][;alternate location][/model ID][@file ID]

Here, residue name and atom name are three letter and four letter name, respectively, and terms in square brackets can be omitted. For example, command 'select SER.CA' selects all alpha carbon atoms in serine. Residue names that contain numeric characters should be enclosed in square brackets such as '[SO4]'. Expressions are treated in a case-insensitive manner. However, the chain ID can be specified case-sensitively such as 'a_A' or 'a_a', where these mean the chains whose auth_asym_id is 'A' or 'a', respectively. In the same way, you can use label_asym_id to specify chains case-sensitively such as 'l_A'. Note that the label_asym_id is available only for PDBML files and not for PDB flat files.