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Atom Sets
RasMol atom expressions may contain predefined sets. These sets are
single keywords that represent portions of a molecule of interest.
Predefined sets are often abbreviations of primitive atom expressions. In
some cases the use of predefined sets allows selection of areas of a
molecule that could not otherwise be distinguished. A list of the
currently predefined sets is given below. In addition to the sets listed
here, RasMol also treats element names (and their plurals) as predefined
sets containing all atoms of that element type, i.e. the command 'select
oxygen' is equivalent to the command 'select
elemno=8'.
The Amino Acid Table summarizes the list of
amino acids corresponding to each set.
This set contains the atoms in the complementary nucleotides adenosine
and thymidine (A and T, respectively). All nucleotides are classified as
either the set 'at' or the set 'cg'
This set is equivalent to the RasMol atom expressions "a,t",
and "nucleic and not cg".
The set of acidic amino acids. These are the residue types Asp and Glu.
All amino acids are classified as either 'acidic', 'basic'
'or' 'neutral'.
This set is equivalent to the RasMol atom expressions "asp,
glu" and "amino and not (basic or neutral)".
The set of atoms in amino acids not containing a cycle or ring. All
amino acids are classified as either 'cyclic'
or 'acyclic'. This set is equivalent to the RasMol atom
expression "amino and not cyclic".
This set contains the aliphatic amino acids. These are the amino acids
Ala, Gly, Ile, Leu and Val. This set is equivalent to the RasMol atom
expression "ala, gly, ile, leu, val".
The set of alpha carbons in the protein molecule. This set is
approximately equivalent to the RasMol atom expression "*.CA".
This command should not be confused with the predefined set 'helix'
which contains the atoms in the amino acids of the protein's alpha
helices.
This set contains all the atoms contained in amino acid residues. This
is useful for distinguishing the protein from the nucleic acid and
heterogeneous atoms in the current molecule database.
The set of atoms in amino acids containing aromatic rings. These are
the amino acids His, Phe, Trp and Tyr. Because they contain aromatic rings
all members of this set are member of the predefined set 'cyclic'.
This set is equivalent to the RasMol atom expressions "his,
phe, trp, tyr" and "cyclic and not pro".
This set contains the four atoms of each amino acid that form the
polypeptide N-C-C-O backbone of proteins, and the atoms of the sugar
phosphate backbone of nucleic acids. Use the RasMol predefined sets 'protein'
and 'nucleic' to distinguish between the two forms of
backbone. Atoms in nucleic acids and proteins are either 'backbone'
or 'sidechain'. This set is
equivalent to the RasMol expression "(protein or nucleic) and
not sidechain".
The predefined set 'mainchain' is synonymous with the
set 'backbone'.
The set of basic amino acids. These are the residue types Arg, His and
Lys. All amino acids are classified as either 'acidic',
'basic' or 'neutral'.
This set is equivalent to the RasMol atom expressions "arg,
his, lys" and "amino and not (acidic or neutral)".
This set contain all the atoms in the current molecule database that
are bonded to at least one other atom.
This set contains the atoms in those amino acids that tend (prefer) to
be buried inside protein, away from contact with solvent molecules. This
set refers to the amino acids preference and not the actual solvent
accessibility for the current protein. All amino acids are classified as
either 'surface' or 'buried'.
This set is equivalent to the RasMol atom expression "amino
and not surface".
This set contains the atoms in the complementary nucleotides cytidine
and guanosine (C and G, respectively). All nucleotides are classified as
either the set 'at' or the set 'cg'
This set is equivalent to the RasMol atom expressions "c,g"
and "nucleic and not at".
This set contains the charged amino acids. These are the amino acids
that are either 'acidic' or 'basic'.
Amino acids are classified as being either 'charged' or 'neutral'.
This set is equivalent to the RasMol atom expressions "acidic
or basic" and "amino and not neutral".
The set of atoms in amino acids containing a cycle or rings. All amino
acids are classified as either 'cyclic' or 'acyclic'.
This set consists of the amino acids His, Phe, Pro, Trp and Tyr. The
members of the predefined set 'aromatic'
are members of this set. The only cyclic but non-aromatic amino acid is
proline. This set is equivalent to the RasMol atom expressions "his,
phe, pro, trp, tyr" and "aromatic or pro"
and "amino and not acyclic".
This set contains the atoms of cysteine residues that form part of a
disulphide bridge, i.e. half cystines. RasMol automatically
determines disulphide bridges, if neither the predefined set 'cystine'
nor the RasMol 'ssbonds'
command have been used since the molecule was loaded. The set of free
cysteines may be determined using the RasMol atom expression "cys
and not cystine".
This set contains all atoms that form part of a protein alpha helix as
determined by either the PDB file author or Kabsch and Sander's DSSP
algorithm. By default, RasMol uses the secondary structure determination
given in the PDB file if it exists. Otherwise, it uses the DSSP algorithm
as used by the RasMol 'structure'
command.
This predefined set should not be confused with the predefined set 'alpha'
which contains the alpha carbon atoms of a protein.
This set contains all the heterogeneous atoms in the molecule. These
are the atoms described by HETATM entries in the PDB file. These typically
contain water, cofactors and other solvents and ligands. All 'hetero'
atoms are classified as either 'ligand'
or 'solvent' atoms. These
heterogeneous 'solvent' atoms
are further classified as either 'water'
or 'ions'.
This predefined set contains all the hydrogen, deuterium and tritium
atoms of the current molecule. This predefined set is equivalent to the
RasMol atom expression "elemno=1".
This set contains all the hydrophobic amino acids. These are the amino
acids Ala, Leu, Val, Ile, Pro, Phe, Met and Trp. All amino acids are
classified as either 'hydrophobic' or 'polar'.
This set is equivalent to the RasMol atom expressions "ala,
leu, val, ile, pro, phe, met, trp" and "amino
and not polar".
This set contains all the heterogeneous phosphate and sulphate ions in
the current molecule data file. A large number of these ions are sometimes
associated with protein and nucleic acid structures determined by X-ray
crystallography. These atoms tend to clutter an image. All 'hetero'
atoms are classified as either 'ligand'
or 'solvent' atoms. All 'solvent'
atoms are classified as either 'water'
or 'ions'.
All amino acids are classified as either 'small',
'medium' or 'large'.
This set is equivalent to the RasMol atom expression "amino
and not (small or medium)".
This set contains all the heterogeneous cofactor and ligand moieties
that are contained in the current molecule data file. This set is defined
to be all 'hetero' atoms that are
not 'solvent' atoms. Hence this
set is equivalent to the RasMol atom expression "hetero and
not solvent".
All amino acids are classified as either 'small',
'medium' or 'large'.
This set is equivalent to the RasMol atom expression "amino
and not (large or small)".
The set of neutral amino acids. All amino acids are classified as
either 'acidic', 'basic'
or 'neutral'. This set is equivalent to the RasMol atom
expression "amino and not (acidic or basic)".
The set of all atoms in nucleic acids, which consists of the four
nucleotide bases adenosine, cytidine, guanosine and thymidine (A, C, G and
T, respectively). All neucleotides are classified as either 'purine'
or 'pyrimidine'. This set is
equivalent to the RasMol atom expressions "a,c,g,t"
and "purine or pyrimidine". The symbols for RNA
nucleotides (U, +U, I, 1MA, 5MC, OMC, 1MG, 2MG, M2G, 7MG, OMG, YG, H2U,
5MU, and PSU) are also recognized as members of this set.
This set contains the polar amino acids. All amino acids are classified
as either 'hydrophobic' or 'polar'.
This set is equivalent to the RasMol atom expression "amino
and not hydrophobic".
The set of all atoms in proteins. This consists of the RasMol
predefined set 'amino' and common
post-translation modifications.
The set of purine nucleotides. These are the bases adenosine and
guanosine (A and G, respectively). All nucleotides are either 'purines'
or 'pyrimidines'. This set is
equivalent to the RasMol atom expressions "a,g"
and "nucleic and not pyrimidine".
The set of pyrimidine nucleotides. These are the bases cytidine and
thymidine (C and T, respectively). All nucleotides are either 'purines'
or 'pyrimidines'. This set is equivalent to the RasMol
atom expressions "c,t" and "nucleic
and not purine".
This set contains the set of atoms in the currently selected region.
The currently selected region is defined by the preceding 'select'
or 'restrict'
command and not the atom expression containing the 'selected'
keyword.
This set contains all atoms that form part of a protein beta sheet as
determined by either the PDB file author or Kabsch and Sander's DSSP
algorithm. By default, RasMol uses the secondary structure determination
given in the PDB file if it exists. Otherwise, it uses the DSSP algorithm
as used by the RasMol 'structure'
command.
This set contains the functional sidechains of any amino acids and the
base of each nucleotide. These are the atoms not part of the polypeptide
N-C-C-O backbone of proteins or the sugar phosphate backbone of nucleic
acids. Use the RasMol predefined sets 'protein' and 'nucleic'
to distinguish between the two forms of sidechain. Atoms in nucleic acids
and proteins are either 'backbone'
or 'sidechain'. This set is equivalent to the RasMol
expression "(protein or nucleic) and not backbone".
All amino acids are classified as either 'small', 'medium'
or 'large'. This set is equivalent
to the RasMol atom expression "amino and not (medium or large)".
This set contains the solvent atoms in the molecule coordinate file.
These are the heterogeneous water molecules, phosphate and sulphate ions.
All 'hetero' atoms are classified
as either 'ligand' or 'solvent'
atoms. All 'solvent' atoms are classified as either 'water'
or 'ions'. This set is equivalent
to the RasMol atom expressions "hetero and not ligand"
and "water or ions".
This set contains the atoms in those amino acids that tend (prefer) to
be on the surface of proteins, in contact with solvent molecules. This set
refers to the amino acids preference and not the actual solvent
accessibility for the current protein. All amino acids are classified as
either 'surface' or 'buried'.
This set is equivalent to the RasMol atom expression "amino
and not buried".
This set contains all atoms that form part of a protein turns as
determined by either the PDB file author or Kabsch and Sander's DSSP
algorithm. By default, RasMol uses the secondary structure determination
given in the PDB file if it exists. Otherwise, it uses the DSSP algorithm
as used by the RasMol 'structure'
command.
This set contains all the heterogeneous water molecules in the current
database. A large number of water molecules are sometimes associated with
protein and nucleic acid structures determined by X-ray crystallography.
These atoms tend to clutter an image. All 'hetero'
atoms are classified as either 'ligand'
or 'solvent' atoms. The 'solvent'
atoms are further classified as either 'water' or 'ions'.
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