Figure 4
From: Stereochemical errors and their implications for molecular dynamics simulations
The Cispeptide plugin. (A) The main window of the plugin showing the selection options in the top form, identified cis peptide bonds in the center form, and options to move atoms and to relax the structure in the bottom form. (B) Molecular visualization highlighting the selected bond generated by the plugin. (C) The configuration generated upon moving the oxygen atom along the C-O bond. (D) The control window for interactive molecular dynamics used in the correction of unusual configurations.