Hi Ahmad, The MatchMaker dialog has "Further restrict matching to current selection” checkbox options right below where you choose the structures/chains to match, see: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchma...> …so after you specify the reference structure or chain(s), select just the parts of them that you want to use and turn on the options. To select, you could use any of the standard methods: mouse + arrow keys, the “select” command, etc. Example command for model 0 chain A residues 10-22 and model 1 chain A residues 35-47: select #0:10-22.A#1:35-47.A … or if you are using the “matchmaker” or “mmaker” command, you can specify the residue ranges directly in the command as explained here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html#restrict> MatchMaker first makes a sequence alignment and then uses the CA atoms of the sequence-aligned residues. Alternatively, you could use the “match” command to directly specify exactly which atoms you want to use for fitting without using any sequence alignment, see: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> This page discusses the different methods of structure alignment: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Jul 25, 2018, at 9:14 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:

Hello, All the options I see in Matchmaker is based on aligning whole chains. Is it possible to align structures based on a specific secondary structure, like a specific alpha helix for example? How to do so? Thanks in advance.