FirstGlance/Evaluating Protein Crosslinks: Difference between revisions
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===Bonds=== | ===Bonds=== | ||
It is important not to take the bonds displayed by FirstGlance/Jmol literally. [[Atomic coordinate files]] from the [[wwPDB]] do not specify most covalent bonds. Rather, Jmol draws covalent "bond" sticks between atoms wherever two atoms are sufficiently close. In the case of carbon, nitrogen and oxygen, this is wherever a pair of those atoms is separated by ≤1.81 Å<ref name="bondlengths">Actual covalent bond lengths are approximately C-C: 1.4 Å; C-N: 1.4 Å; C-O: 1.4 Å; C=O: 1.2 Å C-S: 1.7 Å ([https://en.wikipedia.org/wiki/Covalent_radius Covalent radii in Wikipedia]).</ref>. In perfectly accurate models, this works correctly, but the errors in [[empirical models]] sometimes lead to bonds being drawn incorrectly. Thus, Jmol may show bond sticks where the reality is a clash, not a bond; and Jmol may fail to show bond sticks between atoms that are believed to be covalently bonded, but are too far apart in the model. | It is important not to take the bonds displayed by FirstGlance/Jmol literally. [[Atomic coordinate files]] from the [[wwPDB]] do not specify most covalent bonds. Rather, Jmol draws covalent "bond" sticks between atoms wherever two atoms are sufficiently close. In the case of carbon, nitrogen and oxygen, this is wherever a pair of those atoms is separated by ≤1.81 Å<ref name="bondlengths">Actual covalent bond lengths are approximately C-C: 1.4 Å; C-N: 1.4 Å; C-O: 1.4 Å; C=O: 1.2 Å; C-S: 1.7 Å ([https://en.wikipedia.org/wiki/Covalent_radius Covalent radii in Wikipedia]).</ref>. In perfectly accurate models, this works correctly, but the errors in [[empirical models]] sometimes lead to bonds being drawn incorrectly. Thus, Jmol may show bond sticks where the reality is a clash, not a bond; and Jmol may fail to show bond sticks between atoms that are believed to be covalently bonded, but are too far apart in the model. | ||
==Case Illustrations== | ==Case Illustrations== | ||