Back to TABLE OF CONTENTSPredefined Sets: A-B C-N P-Z Table of amino acid classes
Predefined 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,
primitive atom expressions, and in some cases of selecting, 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.
AT Set
This set contains the atoms in the complementary DNA nucleotides adenosine and thymidine
(A and T respectively). Substitute u for t with RNA
structures. All nucleotides are classified as either the set at (au)
or the set cg. This set is
equivalent to the RasMol atom expressions "a,t" and "nucleic
and not cg".
Acidic Set
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)".
Acyclic Set
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".
Aliphatic Set
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".
Alpha Set
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.
Amino Set
This set contains all the atoms contained in amino acid residues. This is useful for
distinguishing the protein
from the nucleic acid and
heterogenous atoms in the current molecule database.
Aromatic Set
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 also
members of the predefined set cyclic.
This set is equivalent to the RasMol atom expressions "his, phe, trp, tyr"
and "cyclic and not pro".
Backbone Set
This set contains the four atoms of each amino acid that form the polypeptide N-C-C-O
backbone of proteins, and the atoms in the sugar phosphate backbone of nucleic acids. Use
the RasMol predefined sets protein
and nucleic to
distinguish between these 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.
Basic Set
The set of basic amino acids. These are the residues 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)".
Bonded Set
This set contain all the atoms in the current molecule database that are bonded to at
least one other atom.
Buried Set
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".
Back to TABLE OF CONTENTS
Predefined Sets: A-B C-N P-Z
Table of amino acid classes