ColoRNA is software written in 2006 at the Frank Lab by Jamie LeBarron while we were still in Albany. It was recently revived in Ning Gao’s lab by his student Ningning.
Its purpose is the following: if we have two versions of an RNA structure (given as pdb files), differing as a consequence of conformational changes, and given the secondary structure, then the program is able to determine the distances between corresponding residues and heat-map them onto the secondary structure. That is, very mobile/flexible residues show up in red, moderate ones in yellow and green, very stable ones in blue.
So it is possible, with the aid of the program, to determine which parts of the secondary structure are responsible for the mobility of the 3D structure.
LeBarron, J., Mitra, K., and Frank, J. (2007). Displaying 3D data on RNA secondary structures: coloRNA. J Struct Biol 157, 262-270.