FirstGlance/Evaluating Protein Crosslinks: Difference between revisions
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==Instructions for an Isopeptide Bond== | ==Instructions for an Isopeptide Bond== | ||
1. | 1. Go to [http://firstglance.jmol.org FirstGlance in Jmol] (right click link, open in new tab), and enter [[PDB code]] <b>2xi9</b>. | ||
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<table class="wikitable"><tr><td>[[Image:Fgij-xl1.png]]</td></tr></table> | <table class="wikitable"><tr><td>[[Image:Fgij-xl1.png]]</td></tr></table> | ||
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==Clashes== | ==Clashes== | ||
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 errors in the atomic model that produce [[clashes]]. | 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]]. | ||
For each putative crosslink suggested by FirstGlance, it is the responsibility of the user to evaluate whether it is a real covalent crosslink, or a clash. FirstGlance makes this responsibility clear (see the bottom paragraph in the snapshot under step #4 above). | For each putative crosslink suggested by FirstGlance, it is the responsibility of the user to evaluate whether it is a real covalent crosslink, or a clash. FirstGlance makes this responsibility clear (see the bottom paragraph in the snapshot under step #4 above). | ||