Figure 1.

Testing parameters used to build models with torsion angles. Both box-and-whisker plots indicate the effect on the global CαRMSD (between the original structure and reconstructed model) of specifying precise bond angles and bond lengths instead of using ideal values (Engh and Huber 1991). The R statistical computing environment was used to create all box-and-whisker plots (http://www.rproject.org/). The whiskers are set to either 1.5 the interquartile length or the most extreme data point if it is less. (A) Distribution of the CαRMSD for 1894 native protein structures rebuilt using increasing amounts of native information. The length dependence of the reconstruction routine is shown in the inset. In all of the box plots, we saw longer proteins near the high extremes of CαRMSD and smaller proteins near the lower extremes. (B) The same plot as the previous, except it was created using 1894 idealized protein structures.