<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Okay, though in your example file the alignment is kind of trivial since the query and template are identical. Nonetheless, here is a simple Python script that will read I-Tasser PDB files and show the alignment. You run the script by giving Chimera the startup command-line arguments: --script "tasser.py threading1.pdb" (assuming both the script and the PDB file are in the folder you are currently in). You can also provide more than one of the PDB files if you want it to show several alignments. For more info about starting Chimera from the command line, go to this page:<div><br></div><div><a href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/startup.html">http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/startup.html</a></div><div><br></div><div>--Eric</div><div><br></div><div></div></body></html>