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Figure 7
Unacceptable ways of getting rid of a Cβ deviation without fixing the actual problem. (a) Thr101 in PDB entry 1bkr as deposited, with a huge Cβd of 0.63 Å (not shown as a sphere because it obscures the side chain), clashes, a rotamer outlier, the heavier Oγ branch in the lower electron-density peak and the Cβ out of density, all of which are caused by modeling the side chain χ1 180° backwards. (b) CDL/E&H makes the geometry perfect but places the Oγ far out of density. (c) Amber places all three side-chain atoms into peaks by making the chirality at Cβ incorrect. (d) A refit in the correct rotamer replaces clashes with hydrogen bonds, has no outliers and puts each atom into its correct density peak.

Journal logoSTRUCTURAL
BIOLOGY
ISSN: 2059-7983
Volume 76| Part 1| January 2020| Pages 51-62
https://doi.org/10.1107/S2059798319015134
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