Pre-defined Sets

The following pre-defined sets are included, and may be used in the r= selection command. The definitions for these sets are largely borrowed from RasMol.

• r=aliphatic: ALA, GLY, LEU, VAL, ILE, PRO
• r=hydroxyl: SER, THR, TYR
• r=sulfur: CYS, MET
• r=aromatic: TYR, HIS, TRP, PHE
• r=charged: ASP, GLU, ARG, LYS
• r=amide: GLN, ASN
• r=hydrophobic: ALA, GLY, LEU, VAL, ILE, PRO, MET, PHE, TRP
• r=polar: SER, THR, CYS, TYR, HIS, ASP, GLU, ASN, GLN, ARG, LYS
• r=neutral: ALA, GLY, LEU, VAL, ILE, PRO, SER, THR, CYS, MET, PHE, TYR, TRP, ASN, GLN
• r=acidic: ASP, GLU
• r=basic: ARG, LYS
• r=small: ALA, GLY, SER
• r=medium: VAL, PRO, THR, CYS, ASP, ASN
• r=large: ILE, MET, PHE, TYR, HIS, TRP, GLU, GLN, ARG, LYS
• r=cyclic: HIS, PRO, TYR, TRP, PHE
• r=dna: ADE, A, GUA, G, CYT, C, THY, T, URA, U
• r=aa: all amino acids
• r=at: ADE, A, THY, T, URA, U
• r=cg: CYT, C, GUA, G
• r=purine: ADE, A, GUA, G
• r=pyrimidine: CYT, C, THY, T, URA, U
• r=wat: WAT, H2O, HOH, TIP, SOL
• r=substrate: this is defined as r<>wat,r<>aa,r<>dna.

The following are also valid for r=, but are defined at run-time.

• r=helix:
• r=sheet:
• r=turn:
• r=coil: