The gel rectification procedure used in SAFA to help visualize lane and band boundary assignments. (A) A region of a nucleic acid footprinting gel mildly distorted by salt effects and temperature variations; the lane and band boundaries (black lines) are not straight lines, making their assignment difficult. (B) Final visualization of the same gel after a rectifying transformation that maps lane and band boundaries to vertical and horizontal lines. The gel image is taken from a hydroxyl radical footprinting gel for the P4-P6 RNA domain from the Tetrahymena group I ribozyme (Takamoto et al.). The lanes contain an untreated sample in 1; ribonuclease T1 digests as reference ladders in 2, 20, 11, and 21; and footprinting reactions in the presence of 10 mM sodium cacodylate, pH 7.0, and 0.1 mM EDTA plus the following ion concentrations in lanes 3–19: none, 1 mM MgCl2, 10 mM MgCl2, 100 mM MgCl2, 2 M NaCl, 1.5 M NaCl, 1 M NaCl, 0.7 M NaCl, none, 0.5 M NaCl, 0.3 M NaCl, 0.15 M NaCl, 0.10 M NaCl, 0.08 M NaCl, 0.04 M NaCl, 0.02 M NaCl, none.