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

Polar 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".

Protein Set
The set of all atoms in proteins. This consists of the RasMol predefined set amino and common post-translational modifications.

Purine Set
The set of purine nucleotides. These are the nucleotides, 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".

Pyrimidine Set
The set of pyrimidine nucleotides. These are the nucleotides, cytidine and thymidine, or uridine (C and T or U respectively). All nucleotides are either purines or pyrimidines. This set is equivalent to the RasMol atom expressions "c,t" or "c,u" and "nucleic and not purine".

Selected Set
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.

Sheet Set
This set contains all atoms that form part of a protein beta sheet 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.

Sidechain Set
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".

Small Set
All amino acids are classified as either small,medium or large. The small amino acids are: Ala, Gly, and Ser. This set is equivalent to the RasMol atom expression "amino and not (medium or large)".

Solvent Set
This set contains the solvent atoms in the molecule coordinate file. These are the heterogenous water molecules, phosphate and sulfate 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".

Surface Set
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".

Turn Set
This set contains all atoms that form part of a protein turn 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.

Water Set
This set contains all the heterogenous 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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    Predefined Sets:   A-B     C-N     P-Z     Table of amino acid classes