pymol.cmd.align("%s" % name_struct1, "%s" % name_struct2) 

should return a list, the first element of which is the rms, if I remember correctly.
Warren can probably say what the rest of the elements are.

On this note, maybe we could start documenting on the wiki what exactly all these commands return.  It would be very useful for scripting.


Thank you very much Warren,

Now I have a question about PyMOL api,  because when I align two structures, the outpur (rms value) is printed in te screen, but I need to store that value into a variable, is that possible?

I mean, when I do this:"align %s, %s" %(name_struct1, name_struct2) )

How can I get the rms value into a variable?