I'm using cartoon putty to display rmsd between an enzyme with and without ligand. I've got two enzymes (that is four structures all in all) and have prepared two figures. The problem is that the extreme rmsd values vary; in one figure it goes from 0.1 to 1.66 while in the other it goes from 0.1 to 2.33. It seems that the rmsd values are normalized by putty, so that the figures only allow me to compare the distribution of rmsd values in each set of structures, not the actual values.How do I put the two figures on the same scale, so that I can compare them quantitatively?
I've tried to play around with the scale range parameters with little luck.
Any help will be much appreciated,