Load homologous proteins

Select two homologous proteins such as 1df7 and 8dfr (hint to remove existing models: from the Edit menu select For all data and Close).

To set a suitable colour and display style for all models open the Picture wizard window from the Applications menu. In the picture wizard window select colour molecule from the bonds folder in the list at the top of the window. Click the Create picture button to redraw the scene.

Superpose

From the Applications pull-down menu select Superpose.



In the new window check that the Superpose mode (at the top of the window) is Automatic secondary structure matching(SSM) and hit the Superpose button. The models will be superposed. To show the equivalent residues and distances between CA atoms toggle on the button labelled Show matchs between...

Multiple homologous chains

You can also try superposing the 4dfr structure which contains two equivalent chains - if you want to treat these as two separate models load two copies of 4dfr and in the Atom selection column for the first copy select Chains and select chain A. Similarly select chain B for the second copy of 4dfr. The Superpose proteins window should now list the two 4dfr models - for each of them click the button labelled 'All atoms' and select As display object and select the name of the chain. Now click the Superpose button.

Non-homologous proteins

This application will also make a good job of superposing non-homologous structures - it will overlay any similar pattern of secondary structure elements that can be found and the possible alternative matches can be reviewed.