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Figure 3
An example RABDAM input file. It directs RABDAM to perform BDamage analysis for the PDB structures 2blp and 2blz [low- and high-dose structures, respectively, of ribonuclease A (Nanao et al., 2005BB11)], writing the output files to the user-specified directory `Damaged_RNase', and highlighting atoms 194, 645, 310, 730, 446, 845, 496 and 547 (these are the sulfur atoms of the di­sulfide-forming cysteine residues) on the output BDamage kernel density estimate produced for each structure. The input file also instructs RABDAM to skip to the next structure if it encounters any recognized program errors whilst analysing the current structure and to overwrite any previously existing files of the same name and located in the same directory as the output files written during the program run.

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