Back to TABLE OF CONTENTSPredefined Sets:  A-B  C-N   P-Z   Table of amino acid classes

CG Set
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 (au) or the set cg. This set is equivalent to the RasMol atom expressions "c,g" and "nucleic and not at" (DNA) or "nucleic and not au" (RNA).

Charged Set
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".

Cyclic Set
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".

Cystine Set
This set contains the atoms of cysteine residues that form part of a disulfide bridge, i.e. half cystines. RasMol automatically determines disulfide 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".

Helix Set
This set contains all atoms that form part of a protein alpha helix as determined by either the PDB file author or the Kabsch and Sander DSSP algorithm [8]. 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.

Hetero Set
This set contains all the heterogenous 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 heterogenous solvent atoms are further classified as either water or ions.

Hydrogen Set
This predefined set contains all the hydrogen and deuterium atoms of the current molecule. This predefined set is equivalent to the RasMol atom expression "elemno=1".

Hydrophobic Set
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".

Ions Set
This set contains all the heterogenous 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.

Large Set
All amino acids are classified as either small, medium, or large. The large amino acids are: Arg, Glu, Gln, His, Ile, Leu, Lys, Met, Phe, Trp, and Tyr. This set is equivalent to the RasMol atom expression "amino and not (small or medium)".

Ligand Set
This set contains all the heterogenous cofactor and ligand moieties that are contained in the current molecule data file. At 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".

Medium Set
All amino acids are classified as either small, medium or large. The medium amino acids are: Asn, Asp, Cys, Pro, Thr, and Val. This set is equivalent to the RasMol atom expression "amino and not (large or small)".

Neutral Set
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)".

Nucleic Set
The set of all atoms in nucleic acids, which consists of the four nucleotides, adenosine, cytidine, guanosine and thymidine, or uridine (A, C, G and T or U respectively). All nucleotides are classified as either purine or pyrimidine. This set is equivalent to the RasMol atom expressions "a,c,g,t" for DNA and "purine or pyrimidine".
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    Predefined Sets:   A-B     C-N     P-Z     Table of amino acid classes