Hi John, If you mean the structures are superimposed (as far as you know) but outside the view, use "Actions... Focus" in the menu or the command "focus" to bring them into view. Matchmaker keeps the "reference" structure in place, so if you have positioned one of the structures the way you want beforehand, specify that one as the reference in Matchmaker. If you mean that the structures are in view, but not superimposed the way that you want, you try varying the Matchmaker alignment parameters. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/ matchmaker.html> ...more examples of using Matchmaker are in this tutorial: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ alignments.html> Here are some other related tools that might be useful: (A) MD Movie (trajectory viewer) can calculate and display an all- frame-by-all-frame RMSD map, where low->high values are shown with grayscale color coding. See "RMSD Analysis" in the following: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/ framemovie.html> (B) Ensemble Match can calculate all-by-all RMSDs and superpositions for two ensembles each opened as a multi-model PDB file. This is what you get when you open an NMR structure from the PDB, for example. It can compare an ensemble to itself, or to a single protein (it doesn't have to be two different ensembles). You wouldn't want to use this on a very large ensemble, that is with more than about 20 members. For large ensembles, the MD Movie approach above would be better. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ ensemblematch/ensemblematch.html> Both those tools are under Tools... MD/Ensemble Analysis in the menu. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 1, 2009, at 8:08 AM, Beale, John wrote:

Hello,

I am trying to compare a protein structure generated through molecular dynamics to a reference structure that is the starting pdb file. I was using MATCHMAKER. I get the rms value and the residue matches, but when I do this I don’t get the overlaid reference and MD structure in the viewing window. Can someone tell me what I need to do to get the overlaid structures?

Thanks!

John