People who run molecular simulations quickly become familiar with all of the things about a PDB file – missing residues, missing heavy atoms in residues, missing hydrogens, non-standard amino acids, multiple conformations, crystallization ligands, etc. – that might need to be fixed before setting up a simulation. This blog post is a reminder to check, after you have “fixed” your PDB, if you have accidentally introduced aberrant cis peptide bonds into your structure during rebuilding.