Wow! Thanks for all the suggestions, many of them sent off-line. It's going to take me a while to work through all of them to see which are most suitable, but I will report back to the bulletin board with a summary and evaluation when I get to that point.
A couple of thoughts, perhaps premature... Comparing multiple structures that are homologous but not identical is much harder than either comparing multiple copies of the same structure or comparing a single pair of non-identical structures. Combining pairwise deviations does not get you to a net RMSD corresponding to joint optimization of multiple structures. From my preliminary reading of various documentation, it seems that some of the scripts or programs suggested gloss over this point. The list of suggestions so far includes theseus SSM/PDBeFold/LSQMAN Profit ESCET ddmp MOLMOL various private scripts I have not had time to look at yet Please continue to add to the list if you have other ideas. I think the most promising suggestion I have looked at so far is THESEUS, which I must admit I was totally unfamiliar with. http://www.theseus3d.org/ Thanks to Douglas Theobald for bringing it to my attention. [ Now if I can just get over the initial hurdle that this program seems to use every letter of the alphabet, upper and lower case, as a separate command line option.... It is in neck-and-neck competition with gnu tar for the gold medal in 'most options'. ] Ethan On Monday 22 February 2010 17:31:26 Ethan Merritt wrote: > Hi all, > > I am comparing 4 very similar (<1.5A rmsd) large (750 residues) structures, > but struggling to find a way to generate a figure that conveys where they > are most alike and where they diverge. > > Simply drawing a superimposed set of backbone traces results in what looks > like colored spaghetti. I don't think that's going to work. > > So I had the idea of drawing a single backbone trace, or ribbon diagram, > and coloring by the RMSD of the four C-alphas at each residue position. > But I can't find a program that will output this as a table of numbers > I can use. All of the multiple structure superposition programs must > have this information internally. After all, that's what they are minimizing. > But do any of the programs provide an option to write it out? > > I can get pairwise per-residue deviations by doing SSM superposition in Coot, > but that doesn't get me to an RMSD for all four structures jointly. > > Ethan -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742
