Hydrogen in macromolecular models: Difference between revisions
Eric Martz (talk | contribs) |
Eric Martz (talk | contribs) |
||
| Line 4: | Line 4: | ||
==Absence of Hydrogen Atoms in Most Macromolecular Models== | ==Absence of Hydrogen Atoms in Most Macromolecular Models== | ||
Hydrogen atoms are absent from most molecular models in Proteopedia, which come mostly from the [[Protein Data Bank]]. This is because most macromolecular crystals do not have sufficient [[resolution]] to determine the positions of hydrogen atoms. However it is easy to [[#Adding Hydrogens|add hydrogen atoms]], and in fact it is a good idea, because it [[#Model Validation??|helps to correct and validate]] the molecular model. | Hydrogen atoms are absent from most molecular models in Proteopedia, which come mostly from the [[Protein Data Bank]]. 83% of models in the [[Protein Data Bank]] lack hydrogen atoms (in May, 2024). This is because most macromolecular crystals do not have sufficient [[resolution]] to determine the positions of hydrogen atoms. However it is easy to [[#Adding Hydrogens|add hydrogen atoms]], and in fact it is a good idea, because it [[#Model Validation??|helps to correct and validate]] the molecular model. | ||
Although their positions are not well defined empirically in the electron density maps from typical macromolecular crystals, sometimes [[#Adding Hydrogens|hydrogens are added]] to X-ray crystallographic models before they are deposited in the Protein Data Bank. This is the choice of the authors of the [[PDB file]]. Hydrogens are usually present in PDB files resulting from [[NMR]] analysis, and usually present in [[theoretical models]]. | Although their positions are not well defined empirically in the electron density maps from typical macromolecular crystals, sometimes [[#Adding Hydrogens|hydrogens are added]] to X-ray crystallographic models before they are deposited in the Protein Data Bank. This is the choice of the authors of the [[PDB file]]. Hydrogens are usually present in PDB files resulting from [[NMR]] analysis, and usually present in [[theoretical models]]. | ||