FirstGlance/Evaluating Protein Crosslinks: Difference between revisions

1. Go to [http://firstglance.jmol.org FirstGlance in Jmol] (right click link, open in new tab), and enter [[PDB code]] <b>2xi9</b>.

FirstGlance suggests the presence of a "putative crosslink" based solely on the distances between relevant atoms (click the link '''Detailed Methods''' in FirstGlance). Sometimes, instead of a real covalent bond crosslink, the proximity of the relevant atoms is due to [[alternate locations]] or small errors in the atomic model that produce [[clashes]].

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 &le;1.81 &Aring; (for actual bond lengths, see footnote<ref name="bondlengths">Actual covalent bond lengths are approximately C-C: 1.4 &Aring;; C-N: 1.4 &Aring;; C-O: 1.4 &Aring;; C=O: 1.2 &Aring;; C-S: 1.7 &Aring; ([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.