We provide UCSF Chimera extension for displaing the reference alignments. The extension can also be used for calculating pairwise and multiple alignments with our psc++ software. Note that psc++ is still under development. A (preliminary) manual is packed with the extension or can be obtained here. The extension requires chimera build 2540 or newer.
Quick installation guide:
Log in as the user who owns the Chimera-installation!
For Linux and Windows you need to know the name of the Chimera base directory. The save way to find the name is to start chimera, open the IDLE (Menu Favorites), and execute at the IDLE prompt:
import os ; print os.environ['CHIMERA']
To use the extension for viewing the reference structural alignments you need to download the xml files and the corresponding pdb files from this server. Unzip the xml files and the pdb files and move everything into a single directory. Start chimera, open the menu Tools -> Psc++ -> Load XML File. Use the Browse button to open an reference alignment XML file. Once the file is loaded, press Apply. For further details please consult the viewer extension manual.