On Nov 28, 2011, at 4:03 PM, Jacob Keller wrote:
Let me refine my question (sorry for my lack of clarity): is there a program that will output the distances between the corresponding ca's of a superposition on a residue-by-residue basis, and not just a global RMSD value (doubtless these numbers are part of the superposition algorithm itself)? I want to plot these values as a function of residue number to show which parts of the structures deviate more or less from each other.
If you use the MatchMaker tool in UCSF Chimera to make the superposition, it has an option to show the corresponding sequence alignment. The sequence alignment will have an "RMSD" header running across the top, which is a bar graph of the RMSD values. You can the alignment's Headers->Save... menu item to save the numerical values to a file if you want.
If you already have the structures superimposed on your own, you can use Chimera's Match->Align tool to create a superposition-based sequence alignment, and do the same thing with its RMSD header.
Some links: Chimera home page: http://www.cgl.ucsf.edu/chimera alignment tool's RMSD header: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/multalignviewer/multalignviewer.html#assessment --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
