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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



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