Definition of Keywords and Functions

The keywords available for selecting atoms in VMD are listed in tables 5.5 and 5.6 at the end of this chapter. If a keyword definition is followed by bool, it is either on or off. If followed by str it takes a value in the string context. If followed by num it takes a value in the number context.

Table 5.5: Atom selection keywords.

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,	bool	all atoms with the resname H2O, HH0, OHH, HOH,
waters		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
user	float	time-varying user-specified value
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

Table 5.6: Atom selection keywords (continued).

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	str	translates Rasmol selection string 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 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 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 less 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