Ligand: Difference between revisions
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Many visualization and modeling programs further divide hetero atoms into solvent and non-solvent atoms. Solvent includes water and common anions such as sulfate and phosphate. These programs (e.g. RasMol, Chime, and Jmol) often define ligand to include '''all non-solvent hetero atoms'''. In these programs, selecting and displaying ligand will display, for example, '''all carbohydrate''', whether or not covalently linked to a protein, in addition to moieties ordinarily considered to be ligand, such as metal ions and small organic compounds other than [[Standard Residues|standard residues]]. | Many visualization and modeling programs further divide hetero atoms into solvent and non-solvent atoms. Solvent includes water and common anions such as sulfate and phosphate. These programs (e.g. RasMol, Chime, and Jmol) often define ligand to include '''all non-solvent hetero atoms'''. In these programs, selecting and displaying ligand will display, for example, '''all carbohydrate''', whether or not covalently linked to a protein, in addition to moieties ordinarily considered to be ligand, such as metal ions and small organic compounds other than [[Standard Residues|standard residues]]. | ||
Depending on the way in which the PDB file is structured, ''ligand'' can include either an '''entire | Depending on the way in which the PDB file is structured, ''ligand'' can include either an '''entire phosphoserine residue''' [[because that is a [[Non-Standard Residue|non-standard residue]], or '''only the covalently linked phosphate'''. For example, in [[1apm]] the ''phosphite ions'' [PO3] are covalently linked to phosphoserine and phosphothreonine, whereas in [[1bkx]] the same entities are deemed [SEP] and [TPO] ''ligands''. | ||
On the other hand, some things that would ordinarily be considered to be ligands will '''fail''' to be included when ''ligand'' is selected and displayed in Jmol (or RasMol or Chime). These include single amino acids or nucleotides, peptide ligands, DNA or RNA bound to a protein as ligands. | On the other hand, some things that would ordinarily be considered to be ligands will '''fail''' to be included when ''ligand'' is selected and displayed in Jmol (or RasMol or Chime). These include single amino acids or nucleotides, peptide ligands, DNA or RNA bound to a protein as ligands. | ||