[modeller_usage] salign: specify chains to superpose

[Yingjie Lin <Yingjie.Lin AT mssm.edu>]

Hi Modellers,

I wonder what is the best way to superpose two multi-chain proteins, and explicitly specify the chains to include in superposition. I know that I can read only the wanted chains into the alignment, but I also want to make sure that the other chains move according to the superposition.

Here are two ways we could think of:
1. read only the wanted chains and do superposition.
 Then move the other chains accordingly using functions like selection.rotate_origin(), selection.rotate_mass_center() and selection.transform().

2. 
model1 <= all chains in protein A
model2 <= all chains in protein B
model3 <= the chain(s) selected for superposition in protein B
first, superpose model3 to model1 (model3 is moved)
second, superpose model2 to model3 (model2 is moved)

Are there any better ways? Thank you.

Yingjie