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Atom Expressions
RasMol atom expressions uniquely identify an
arbitrary group of atoms within a molecule. Atom expressions are composed of either
primitive expressions, predefined sets, comparison operators, within
expressions, or logical (boolean) combinations of the above expression types.
The logical operators allow complex queries to be constructed out of simpler
ones using the standard boolean connectives and, or and not.
These may be abbreviated by the symbols "&", "|"
and "!" respectively. Parentheses (brackets) may be used to
alter the precedence of the operators. For convenience, a comma may also be used for
boolean disjunction.
The atom expression is evaluated for each atom, hence protein and
backbone selects protein backbone atoms, not the protein and [nucleic] acid
backbone atoms!
Examples: backbone and not helix
within( 8.0, ser70 )
not (hydrogen or hetero)
not *.FE and hetero
8, 12, 16, 20-28
arg, his, lys
Examples
Primitive Expressions
Comparison Operators
Within Expressions
Example Expressions
The following table gives some useful examples of
RasMol atom expressions.
Expression Interpretation
* All atoms
cys Atoms in cysteines
hoh Atoms in heterogenous water molecules
as? Atoms in either asparagine or aspartic acid
*120 Atoms at residue 120 of all chains
*p Atoms in chain P
*.n? Nitrogen atoms
cys.sg Sulfur atoms in cysteine residues
ser70.c? Carbon atoms in serine-70
hem*p.fe Iron atoms in the Heme groups of chain P
Primitive Expressions
RasMol primitive expressions are the fundamental
building blocks of atom expressions. There are two types of primitive expression.
A residue name typically consists of up to three alphabetic characters,
which are case insensitive. Hence the primitive expressions SER and ser
are equivalent, identifying all serine residues. Residue names that contain non-alphabetic
characters, such as sulfate groups, may be delimited using square brackets, i.e.[SO4]
The residue number is the residue's position in the macromolecule sequence.
Negative sequence numbers are permited. For example, SER70. Care must be
taken when specifying both residue name and number: if the group at the specified position
isn't the specified residue no atoms are selected.
The chain identifier is typically a single case-insensitive alphabetic or
numeric character. Numeric chain identifiers must be distinguished or separated from
residue numbers by a colon character. For example, SER70A or SER70:1
The second part consists of a period character followed by an atom name. An
atom name may be up to four alphabetic or numeric characters.
An asterisk may be used as a wild card for a whole field and a question mark as a single
character wildcard. Multiple NMR Models in PDB files:
The syntax of RasMol atom expressions allows the selection of individual molecule
conformations if present in an NMR file. The simplest form of the atom expression
is the syntax "::25" to select model 25 from the molecule. This is equivalent to
the atom expression, "model = 25", as the keyword model may now be used
in comparison expressions. The most general form of atom expression is now CYS32:A:25.SG
which denotes the gamma sulfur of residue cysteine-32 in chain A of model 25.
Individual chains may be specified by the syntax ":A" for chain A,
or ":1" for chain 1 (i.e. the wildcard may be dropped from the expression
"*:A"). This may also be extended to NMR models; ":A:4" denotes chain
A of model 4, and even more terse, "::4" means all atoms in all chains of NMR
model 4.
Comparison Operators
Parts of a molecule may also be distinguished
using equality, inequality and ordering operators on their properties. The format of such
comparison expression is a property name, followed by a comparison operator and then an
integer value.
The atom properties that may be used in RasMol are atomno
for the atom serial number, elemno for the atom's atomic number (element),
resno for the residue number, radius for the spacefill
radius in RasMol units (or zero if not represented as a sphere) and temperature
for the PDB anisotropic temperature value.
The equality operator is denoted as either = or ==.
The inequality operator is either <>, !=, or /=.
The ordering operators are: < for less than; <=
for less than or equal to; > for greater than; and >=
for greater than or equal to.
Examples: resno 23
temperature >= 900
atomno == 487
Within Expressions
A RasMol within expression allows
atoms to be selected on their proximity to another set of atoms. A within
expression takes two parameters separated by a comma and surrounded by parentheses. The
first argument is an integer value called the "cut-off" distance of the within
expression and the second argument is any valid atom expression. The cut-off distance is
expressed in either integer RasMol units or Angstroms containing a decimal point. An atom
is selected if it is within the cut-off distance of any of the atoms defined by the second
argument. This allows complex expressions to be constructed containing nested within
expressions.
For example, the command select within(3.2,backbone)
selects any atom within a 3.2 Å radius of any atom in a protein or nucleic acid backbone.
Within expressions are particularly useful for selecting the atoms around
an active site.
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