Definition of Keywords and Functions

Keyword Arg Description

all bool everything

none bool nothing

name str atom name

type str atom type

index num the atom number, starting at 0

chain str the one-character chain identifier

residue num a set of connected atoms with the same residue number

protein bool a residue with atoms named C, N, CA, and O

nucleic bool a residue with atoms named P, O1P, O2P and either

O3', C3', C4', C5', O5' or O3*, C3*, C4*, C5*, O5*.

This definition assumes that the base is phosphorylated,

an assumption which will be corrected in the future.

backbone bool the C, N, CA, and O atoms of a protein

and the equivalent atoms in a nucleic acid.

sidechain bool non-backbone atoms and bonds

water, waters bool all atoms with the resname H2O, HH0, OHH, HOH,

OH2, SOL, WAT, TIP, TIP2, TIP3 or TIP4

fragment num a set of connected residues

pfrag num a set of connected protein residues

nfrag num a set of connected nucleic residues

sequence str a sequence given by one letter names

numbonds num number of bonds

resname str residue name

resid num residue id

segname str segment name

x, y, z float x, y, or z coordinates

radius float atomic radius

mass float atomic mass

charge float atomic charge

beta float temperature factor

occupancy float occupancy

at bool residues named ADA A THY T

acidic bool residues named ASP GLU

acyclic bool ``protein and not cyclic''

aliphatic bool residues named ALA GLY ILE LEU VAL

alpha bool atom's residue is an alpha helix

amino bool a residue with atoms named C, N, CA, and O

aromatic bool residues named HIS PHE TRP TYR

basic bool residues named ARG HIS LYS

bonded bool atoms for which numbonds>0

buried bool residues named ALA LEU VAL ILE PHE CYS MET TRP

cg bool residues named CYT C GUA G

charged bool ``basic or acidic''

cyclic bool residues named HIS PHE PRO TRP TYR

Keyword	Arg	Description
hetero	bool	``not (protein or nucleic)''
hydrogen	bool	name "[0-9]?H.*"
large	bool	``protein and not (small or medium)''
medium	bool	residues named `VAL THR ASP ASN PRO CYS ASX PCA HYP`
neutral	bool	residues named `VAL PHE GLN TYR HIS CYS MET TRP ASX GLX PCA HYP`
polar	bool	``protein and not hydrophobic''
purine	bool	residues named `ADE A GUA G`
pyrimidine	bool	residues named `CYT C THY T URI U`
small	bool	residues named `ALA GLY SER`
surface	bool	``protein and not buried''
helix	bool	atom's residue is an alpha helix
helix_3_10	bool	atom's residue is an alpha helix
extended_beta	bool	atom's residue is a beta sheet
bridge_beta	bool	atom's residue is a beta sheet
rasmol	Rasmol string	translates Rasmol selection syntax to VMD
alpha_helix	bool	atom's residue is an alpha helix
pi_helix	bool	atom's residue is a pi helix
helix	bool	atom's residue is an alpha or pi helix
sheet	bool	atom's residue is a beta sheet ???
turn	bool	atom's residue is in a turn conformation
coil	bool	atom's residue is in a coil conformation
structure	str	single letter name for the secondary structure
phi, psi	float	backbone conformational angles
within	str	selects all atoms within a specified distance
		of a selection (i.e `within 5 of name FE`).
exwithin	str	'exclusive within'; equivalent to `(within 3 of X) and not X`.
same	str	selects all atoms which have the same keyword
		as the atoms in a given selection (i.e. `same segname as resid 35`)
ufx, ufy, ufz	num	force to apply in the x, y, or z coordinates

Table 5.7 lists the built-in functions which may be used in atom selection expressions with keywords which take on a numeric value.

Table 5.7: Atom selection functions.

Function	Description
sqr(x)	square of x
sqrt(x)	square root of x
abs(x)	absolute value of x
floor(x)	largest integer not greater than x
ceil(x)	smallest integer not greater than x
sin(x)	sine of x
cos(x)	cosine of x
tan(x)	tangent of x
atan(x)	arctangent of x
asin(x)	arcsin of x
acos(x)	arccos of x
sinh(x)	hyperbolic sine of x
cosh(x)	hyperbolic cosine of x
tanh(x)	hyperbolic tangent of x
exp(x)	``e to the power x''
log(x)	natural log of x
log10(x)	log base 10 of x