Hello, The first thing to understand is that Match->Align requires the protein structures to be superimposed already. That is, you have to superimpose or match the structures (for example, with the “matchmaker” command) BEFORE you use Match->Align. Here is a discussion of the different ways to superimpose structures: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> After the structures are superimposed, then you can consider how to use Match->Align with a script, since it doesn’t have a command. For that, see this previous post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-September/007934.html> If you are only doing pairwise alignments and the structures have fairly similar sequences, another possibility is to just use the sequence alignment created by Matchmaker (or “matchmaker" command with “show true”). For that, see this previous post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-June/010017.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 Aug 10, 2017, at 6:35 AM, sonal rashmi <me.sr1510@gmail.com> wrote:

sir/mam, i want to use chimera Match->Align feature using the commandline or nogui script (python) to align multiple protein sequences (pdb files) to generate the alignment on MultiAlignViewer and save it as clustal (.aln) file. I tried out the python codes posted on the portals but non of them are giving proper alignment. kindly advice as to what i can do? Is there any commandline available for it? Thanking You Sincere User