On Apr 13, 2011, at 4:00 PM, Rex Palmer wrote:
What is the best program to use for comparing two protein structures which are very similar both structurally and wrt aa sequence? ie to get the rms deviations both generally and in selected regions.
Best is kind of subjective, but you can use the MatchMaker tool in Chimera to superimpose the structures and show the superposition. MatchMaker also has an option to show the corresponding sequence alignment. The alignment will have a histogram of the column RMSD values running across the top. You can drag the mouse on the alignment to select/highlight the corresponding parts of the structure and to show the RMSD of the dragged region in the alignment's region- browser window.
MatchMaker described here: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/matchmaker/matchmaker.html Chimera obtainable here: http://www.cgl.ucsf.edu/chimera --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
