Clashes: Difference between revisions

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default [[Tutorial:Ramachandran principle and phi psi angles]]

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''Clashes'' in protein models, also called ''steric clashes'', occur when two ~~non-~~bonded ~~atoms~~ are impossibly close to each other. This happens when the [[van der Waals radii]] of the atoms overlap; that is, when two atoms are occupying the same space. Clashes typically occur in lower [[resolution]] models due to the difficulties of obeying all chemical constraints while optimizing the fit of the model to the experimental data. Clashes are more common in [[X-ray crystallography|X-ray crystallographic]] models with [[resolution|resolutions]] of 3.0 Å or worse, or in [[cryo-EM]] models. ([[NMR]] models generally lack clashes because they are forced to obey chemical constraints.)

''Clashes'' in protein models, also called ''steric clashes'', occur when two atoms, not covalently bonded to each other, are impossibly close to each other. This happens when the [[van der Waals radii]] of the atoms overlap; that is, when two atoms are occupying the same space. Clashes typically occur in lower [[resolution]] models due to the difficulties of obeying all chemical constraints while optimizing the fit of the model to the experimental data. Clashes are more common in [[X-ray crystallography|X-ray crystallographic]] models with [[resolution|resolutions]] of 3.0 Å or worse, or in [[cryo-EM]] models. ([[NMR]] models generally lack clashes because they are forced to obey chemical constraints.)

==Clashes Dictate Protein Secondary Structure==

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 default [[Tutorial:Ramachandran principle and phi psi angles]]
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-''Clashes'' in protein models, also called ''steric clashes'', occur when two non-bonded atoms are impossibly close to each other. This happens when the [[van der Waals radii]] of the atoms overlap; that is, when two atoms are occupying the same space. Clashes typically occur in lower [[resolution]] models due to the difficulties of obeying all chemical constraints while optimizing the fit of the model to the experimental data. Clashes are more common in [[X-ray crystallography|X-ray crystallographic]] models with [[resolution|resolutions]] of 3.0 Å or worse, or in [[cryo-EM]] models. ([[NMR]] models generally lack clashes because they are forced to obey chemical constraints.)
+''Clashes'' in protein models, also called ''steric clashes'', occur when two atoms, not covalently bonded to each other, are impossibly close to each other. This happens when the [[van der Waals radii]] of the atoms overlap; that is, when two atoms are occupying the same space. Clashes typically occur in lower [[resolution]] models due to the difficulties of obeying all chemical constraints while optimizing the fit of the model to the experimental data. Clashes are more common in [[X-ray crystallography|X-ray crystallographic]] models with [[resolution|resolutions]] of 3.0 Å or worse, or in [[cryo-EM]] models. ([[NMR]] models generally lack clashes because they are forced to obey chemical constraints.)
 ==Clashes Dictate Protein Secondary Structure==