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I am pretty sure you can do this using LSQMAN from Gerard (BluRay?) Kleywegt. The pertinent commands are MCENTRAL to determine the 'most representative structure' (i.e. the one to align upon and show in the figure), MALIGN to do the alignment and then MPLOT to calculate a 'multi-RMSD' for each residue (see manual for details - set the 'cut-off for printing' to 0 to get all values). Regards depiction, I think pymol can also represent structures as sausages based on their B values: cartoon putty show cartoon HTH, Stephen On 23 February 2010 01:31, Ethan Merritt <[log in to unmask]> 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 > -- Dr Stephen Graham 1851 Research Fellow Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital, Hills Road Cambridge, CB2 0XY, UK Phone: +44 1223 762 638