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Commands:
arrow1.gif (162 bytes)Using RasTop
arrow1.gif (162 bytes)RasTop World
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arrow1.gif (162 bytes)Summary
arrow1.gif (162 bytes)Reference
arrow1.gif (162 bytes)Internal Parameters
arrow1.gif (162 bytes)Atom Expression
arrow1.gif (162 bytes)Colour Schemes
arrow1.gif (162 bytes)Atom Sets
Content:
AT
Acidic
Acyclic
Aliphatic
Alpha
Amino
Aromatic
Backbone
Basic
Bonded
Buried
CG
Charged
Cyclic
Cystine
Helix
Hetero
Hydrogen
Hydrophobic
Ions
Large
Ligand
Medium
Neutral
Nucleic
Polar
Protein
Purine
Pyrimidine
Selected
Sheet
Sidechain
Small
Solvent
Surface
Turn
Water

 

 

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.


up.gif (892 bytes) AT 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".


up.gif (892 bytes) 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)".


up.gif (892 bytes) 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".


up.gif (892 bytes) 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".


up.gif (892 bytes) 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.


up.gif (892 bytes) 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 heterogeneous atoms in the current molecule database.


up.gif (892 bytes) 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 member of the predefined set 'cyclic'. This set is equivalent to the RasMol atom expressions "his, phe, trp, tyr" and "cyclic and not pro".


up.gif (892 bytes) 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 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'.


up.gif (892 bytes) Basic Set

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)".


up.gif (892 bytes) Bonded Set

This set contain all the atoms in the current molecule database that are bonded to at least one other atom.


up.gif (892 bytes) 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".


up.gif (892 bytes) 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' or the set 'cg' This set is equivalent to the RasMol atom expressions "c,g" and "nucleic and not at".


up.gif (892 bytes) 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".


up.gif (892 bytes) 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".


up.gif (892 bytes) Cystine Set

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".


up.gif (892 bytes) Helix Set

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.


up.gif (892 bytes) Hetero Set

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'.


up.gif (892 bytes) Hydrogen Set

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".


up.gif (892 bytes) 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".


up.gif (892 bytes) Ions Set

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'.


up.gif (892 bytes) Large Set

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)".


up.gif (892 bytes) Ligand Set

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".


up.gif (892 bytes) Medium Set

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)".


up.gif (892 bytes) 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)".


up.gif (892 bytes) Nucleic Set

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.


up.gif (892 bytes) 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".


up.gif (892 bytes) Protein Set

The set of all atoms in proteins. This consists of the RasMol predefined set 'amino' and common post-translation modifications.


up.gif (892 bytes) Purine Set

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".


up.gif (892 bytes) Pyrimidine Set

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".


up.gif (892 bytes)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.


up.gif (892 bytes) Sheet Set

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.


up.gif (892 bytes) 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".


up.gif (892 bytes) Small Set

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)".


up.gif (892 bytes) Solvent Set

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".


up.gif (892 bytes) 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".


up.gif (892 bytes) Turn Set

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.


up.gif (892 bytes) Water Set

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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Last updated on Saturday, December 29, 2001