C validating tutorial
As you can see for 3dnd, both RMSD-bonds and RMSD-angles are a bit large, which could indicate some misfit areas of the structure that are causing geometric strain.Close the "POLYGON" window and return to the comprehensive validation window. When Coot loads, note that it says "Connected to PHENIX" in the toolbar - this allows the validation GUI to communicate with Coot. Under this tab, you will see sub-tabs for "Summary", "Basic geometry", "Protein", and "Clashes".
Misfit sidechains will often have multiple diagnostic indicators of a problem, which is useful in easily identifying the worst offenders.
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As you can see in Coot, this orientation is not a terrible fit to the density - but it is a rotamer outlier and energetically unfavorable due to an eclipsed Chi angle, and it has a suggestive difference peak. In Coot, click Calculate- Model/Fit/Refine to bring up the window of modeling tools.
First, we need to select a map, which you can do by pressing the "Select Map" button. Next, select "Auto Fit Rotamer", and then click on an atom in the Leu A 27 sidechain. These kinds of misfit Leu residues are common in crystal structures, but are easy to identify and fix.