1. Prepare your files. Chimera may get a bit confused if sequence numbering is messed up, so remove all the things you don't actually need (e.g. waters) and make sure the initial and final conformation have perfectly aligned sequences. | 1. Prepare your files. Chimera may get a bit confused if sequence numbering is messed up, so remove all the things you don't actually need (e.g. waters) and make sure the initial and final conformation have perfectly aligned sequences. |