Q.820 - Can I make a CA-CA distance plot of my protein(s) ?

Category: S.820 - analysis

Use MOLEMAN, CA_D. This is an almost forgotten tool in these days of interactive 3D graphics and YASSPA and DSSP, but it deserves better than that. Plot the file produced by MOLEMAN with O2D and immediately you'll see where you have helices and strands AND whether they are close to one another AND whether or not they run in parallel. In addition, if you have a protein-protein complex, you'll see at once which residues in one protein are close to which residues in the other protein !